Did Savage Opress become evil of his own free will, or are his evil acts the product of the Nightsisters' brainwashing? Or some combination of the two? Savage's death scene only serves to further muddy the issue.
Is Darth Maul a Woobie, Destroyer of Worlds who acts the way he does because of all of the hardships he's endured throughout his life and for all of his evil genuinely cares about his brother? Or is he an utterly unsympathetic villain whose obsession with Obi-Wan has turned him into revenge-fueled psychopath that treats his brother (who he starts referring to solely as "apprentice") as a minion and an investment? There's arguments that can be made for both. Maul's reaction to Savage's death seems to suggest that he did care about his brother, albeit in a cold, detached, Jerk with a Heart of Gold sort of way.
In a similar vein, her mourning one of the Jedi who were killed in the bombing she masterminded. Was she merely acting, or is she showing some genuine remorse? Likewise, was her conversation with Ahsoka after the memorial service manipulation, or was she having doubts about her choices? The look of sorrow and guilt on her face as Ahsoka walks away suggests the latter, but her later actions imply the former. In the end, it's most likely both, she was actively manipulating Ashoka but still felt remorseful about having to do it, reinforced by the sad look she gives Ashoka after being exposed and arrested at the end of the arc.
Her comment that she feels Asajj's lightsabers suit her muddies the waters even more. Only Sith use red lightsabers, after all.
Ahsoka's decision to leave the Order. Did she do it because she realised that Barriss had a point about the growing corruption of Order's values and morals? Or was she simply too hurt by the way she had been betrayed by Barriss and abandoned by the Council? By extension, was it the mature thing to do, or a selfish child's "self-pity"? While the first option appears to be more popular among fans, some argue it was the latter.
Animation Age Ghetto: Played straight and then averted. The movie and many first-season episodes possess many "childish" attempts that are also seen in the first two prequels, which goes hand-in-hand with George Lucas' various comments that Star Wars is for kids. However, the series played with darker themes and more intense violence in a few episodes such as "Rookies", and by the time the season ended, The Clone Wars adopted the more mature, less whimsical tone that it became known (and praised) for, remaining safe for older children to watch but playing out like your average action blockbuster.
Audience-Alienating Premise: The series will win you over with its artistic excellence, but it has to do so with a potentially debilitating premise. Namely, for all the heroes' wisdom and daring do, they are all a bunch of suckers fooled by Palpatine who is manipulating both sides to weaken them in order to finally seize power in Revenge of the Sith, whereupon nearly all of the Jedi will die.
Bringing Darth Maul back from the dead, for those who thought he was underutilized and killed off too early in The Phantom Menace.
Similarly, bringing Admiral Trench back as a cyborg in the bonus content can be seen as this to those who thought he was killed off too early (for specifics, at the end of his debut episode).
There were complaints that in Revenge of the Sith the mutual distrust between Anakin and the Council felt forced and the conflict underdeveloped, due to neither party having enough reason behind it. The series nicely set things up for this, with the Council lying to Anakin about Obi-Wan Faking the Dead, and abandoning Ahsoka when she got framed.
In a similar vein to the above; the series overall has received a great deal of praise for, arguably, helping to fix Anakin's image in general: his slow but steady and inevitable turn to the Dark Side is allowed to be explored in a much fuller degree and allows for his character development to properly blossom. Tied into that, the much more realistic and natural portrayal of his relationship with Padme really helped to better give audiences the sense that they loved each other as deeply as they say they do in the films.
Some of the story arcs written by Christian Taylor (particularly the Mortis trilogy and the Yoda arc) were most likely written to re-mystify the Force after the Prequels were accused of demystifying it with the introduction of midi-chlorians. While the Mortis trilogy was deliberately mysterious while "Destiny" put a bit more clarification on what midi-chlorians actually are (the link between the living Force and the cosmic Force rather than the cause of the Force itself) and giving them an even more mysterious homeworld. The latter even included a slight jab at the accusations, with the Serene Priestess describing them as "what your science calls 'midi-chlorians'" to Yoda.
Having Ahsoka survive the Clone Wars and not be killed, as many had speculated due to being Doomed by Canon, and giving her a very emotional departure, was highly praised. In addition, it is the decision to have her quit also spared her from Order 66 during the Purge of the Jedi, and allowed her to return later on.
Dave Filoni decided to revive Echo for the incomplete "Bad Batch" arc that debuted at Celebration Anaheim because he felt bad after seeing so many fans feel upset at his death.
Some people felt that Revenge of the Sith created a Continuity Snarl by implying that Qui-Gon Jinn had managed to become a Force ghost after his death. Namely, we see his corpse in The Phantom Menace, despite the fact that Jedi are supposed to lose their physical forms when they become one with the Force (such as Obi-Wan in A New Hope, and Yoda in Return of the Jedi). Qui-Gon was also not seen with the other Force ghosts in Return of the Jedi, even in the updated special editions. Season 6 of The Clone Wars clarified that Qui-Gon had not completed his training before his death, and thus could only manifest himself as a disembodied voice instead of a proper Force ghost.
Award Snub: Dee Bradley Baker's truly amazing work in giving distinct personalities to almost every single clone soldier, through nothing but vocal tones and speech patterns was nominated for Annie award, exactly once.
Awesome Music: Plenty of it. It is Star Wars after all. Notable however, in that the show has plenty of its own Awesome Music made just for the show, rather than always relying on the soundtracks from the movies. Kevin Kiner (the series composer) also has some of the soundtrack released on his own website. 
Out of all the series' retcons to Expanded Universe material, one of the most highly contested is its depiction of the Mandalorians. Is the idea of a Proud Warrior Race culture turning pacifistic a serious case of Badass Decay for them and an insult to how other writers have developed them (also not helped by the fact that what seems to be the only remnants of the warrior culture are a fanatically bloodthirsty terrorist cult)? Or is it a much-needed reality check for the historical progression of the culture (as well as how the warrior culture would be viewed by outsiders) after Karen Traviss'sdepictionof it proved controversial even to some Legends fans. Even after the New Mandalorian government came crumbling down near the end of the series, this series' depiction (as well as the current canon's) of Mandalorians is still contested territory, and the Legends decision (which, until the reintroduction of the Protectors in Star Wars Rebels, effectively erased almost all aspects of the old Mandalorian from canon) didn't help this debate very much.
Bellisario's Maxim: The season one episode "Trespass", which occurred on an ice-world, featured a scene with a group of native Talz huddled around a fire. According to the special features, the writers and producers have been bombarded with questions asking what the Talz were burning, more-so from people involved with the production than even rabid fans, and they can not give an adequate explanation. They quote the maxim almost verbatim, and explain that this is something that people really should not think about.
Better on DVD: The fact that the episodes can be watched on their own at any time means that they can be watched in any order, allowing one to watch the episodes of the first two-and-a-half seasons in chronological order. Bonus points go to the Season 5 box set, where "Revival" (which was aired as the season premiere) is now listed before "Eminence" as was originally intended.
Better Than Canon: While The Clone Wars is canon to the films, the series is widely considered to have done a better job portraying Anakin than the Prequel trilogy; he's genuinely likable despite his flaws, he and Obi-Wan actually come across as the Heterosexual Life-Partners the films tried to paint them as, and his conflicted feelings about the Jedi are rather less Wangst-y. Some even say knowledge of the series' events retroactively improves his portrayal in the prequels to an extents.
This show (especially the first season and the movie) has been very divisive among Star Wars fans who are very sensitive about things that risk interfering with the Expanded Universe, and those who just like everything Star Wars and/or are less sensitive to retcons.
The series being cancelled. Almost everyone's shocked, as the final episodes of the season set up a few more arcs, and Disney is being blamed by almost everyone, but there are a few that feel like the show had run its course, or were happy to see it go.
Captain Obvious Reveal: Barriss Offee being the Jedi temple bomber is not surprising, due to it being foreshadowed out the wazoo, As she's the only other person who Ahsoka talks to other than Ventress during the whole of her escape, and the only other Jedi with a similar build and dark-cloak dress. Not only that, but this was the first time she'd appeared in 3 entire seasons, with every scene suspiciously highlighting her importance.
Catharsis Factor: Even without watching the series, just check out Pong Krell's entry on Complete Monster directly below and you'll know exactly why Dogma shooting him in the back feels so good.
Chancellor Palpatine, aka Darth Sidious, is the instigator of the Clone Wars and the Dark Lord of the Sith. Desiring an army of Force-users to serve his will, Sidious hired Cad Bane to kidnap Force-sensitive infants, so that Sidious could perform horrific and potentially fatal experiments upon them, coldly disregarding their possible deaths. When he felt that Asajj Ventress was growing too powerful, Sidious commanded Count Dooku to kill her, ignoring his protests and mockingly praising his apprentice for his "loyalty" when Dooku believed that he had carried out the order. Later, after deciding that his former apprentice, Darth Maul, had grown too powerful, Sidious attacked him on Mandalore, brutally murdering Maul's brother, Savage Opress, and sadistically torturing Maul himself into submission, later using Maul in a plot to kill Mother Talzin. When Fives discovered Order 66, Palpatine had him drugged into insanity to prevent the truth from being revealed, a plan which ended in Fives's death. When Yoda sets out on a vision quest, Sidious takes the opportunity to try and destroy the vulnerable Jedi Master, using Sith sorcery in an attempt to corrupt and kill Yoda. As always, Darth Sidious is a malevolent, sadistic monster who employs exceptionally cruel methods in his quest for power.
General Pong Krell, introduced in season 4, is a ruthless and treacherous fallen Jedi who only cares for his own survival and benefit. Having foreseen that the Jedi will lose the Clone Wars, Krell sets out to sabotage their efforts in the Battle of Umbara to ingratiate himself with Count Dooku and become the Sith Lord's apprentice. Taking command of the 501st Legion, Krell, who holds Clones in deep contempt, forces his troops into disastrous battle plans designed to kill as many of them as possible. When Jesse and Fives disobey Krell's orders to carry out a successful mission, Krell, after initially deciding to have them court martialled, orders their execution. When the Clones refuse to follow this order, Krell engineers a battle between two batallions of Clones, claiming to each group that the other consists of enemy infiltrators, resulting in several deaths. Exposed as a traitor, Krell rampages through the Clones' ranks, violently killing many of them before being captured. When questioned, Krell admits that, in addition to his plan, he simply enjoyed manipulating and murdering Clones because he found them "inferior." When Rex prepared to execute him for his crimes, Krell taunted the Clone Captain, mocking his emotional turmoil. Sadistic, brutal, and smug to his final breath, Pong Krell is the perfect example of the corrupting influence of war upon the Jedi Order.
Keeper Agruss, also from season 4, is the cruel Zygerrian taskmaster of the Kadavo mining facility. Charged with breaking the will of Obi-Wan Kenobi, Agruss starts by executing several slaves just to make a point to the Jedi Master. Setting his slaves to work in horrible conditions, Agruss has other slaves tortured if Obi-Wan tries to help them, intending to make his help unproductive and alienate those whom Obi-Wan wants to help. When the Republic arrives to free Kenobi and the other slaves, Agruss sets the mining facility's system to drop all of the slaves to their deaths, and smashes the control panel to prevent Obi-Wan from undoing this. Agruss then taunts Obi-Wan by claiming that he cannot retaliate because of his Jedi beliefs, prompting the normally merciful Obi-Wan to subtly order Rex to kill Agruss. Even in a society of slavers, Keeper Agruss is a despicable being who places no value on innocent lives beyond their use to him.
Crazy Awesome: Quinlan Vos is described as being eccentric from the get-go, and he's one of the few Jedi that makes Anakin look subtle. He's also very formidable because of this.
Creator's Pet: Ahsoka Tano was this for the first season, due to being perceived as a Spotlight-Stealing Squad. However, the creators eventually realized that she was getting this treatment from the fans, and subsequently toned down the number of appearances in the remaining seasons (while making sure that the episodes she did appear in were heavy on Character Development), taking her out of this trope.
Darth Sidious, especially as of "The Lawless" where he firmly establish how beyond the show's cast he is, and continues to be the display the same sadism he's known for.
Mother Talzin. She not only revives Asaji after her betrayal by Count Dooku, but she is able to revive a seemingly dead Maul. Bonus points for having the same voice as the infamous Rita Repulsa.
Darth Maul's appearances in the series firmly establish him as a cold-blooded sociopath who cares nothing for murdering innocent people just to spite Obi-Wan. Nevertheless, he remains every bit as badass as he was in The Phantom Menace.
Critical Backlash: Not so much the series, but the movie was nearly universally panned by critics and many long time Star Wars fans, even though it wasn't that bad for a pilot arc.
Grievous: You've been designed for this mission, to be the ultimate infiltration units. Some of you may not return... actually, none of you will. But do not let that stop you from completing your task.
The music throughout "Trespass" is excellent, doing a great job of conveying the intense drama of the tensions between the Talz and Republic soldiers, and lending surprising pathos to the death of Chairman Cho before culminating in the dramatic final confrontation between Thi-Sen and Senator Chuchi.
The music during the latter parts of the "Brain Invaders" episode was particularly memorable with chanting when Ahsoka fights a brainwashed Bariss Offee in the halls of the ship.
The tune to which the Republic marches onto the bridge in "Weapons Factory" was surprisingly epic as well.
"Overlords", the music played while Anakin defeated the Daughter and the Son on Mortis.
The piece that accompanies Darth Sidious' duel with Darth Maul and Savage Opress. It's fittingly epic for a clash between some of (and in Sidious' case, THE) most powerful Dark Side users to ever live.
The music that ended "The Wrong Jedi". It was actually orchestrated and not made on a computer, and it added to the already emotional scene of Ahsoka leaving the Jedi Order.
The opening theme. Recognizably Star Wars, but different enough that you know this something else. With a slightly more militaristic bent, it suits the series perfectly.
There are quite a few fans that dislike Lux because they would rather have Ahsoka paired with someone else.
And quite a few who dislike Rex/Anakin/Barriss/etc. because they want her paired with Lux. It never ends.
Anakin/Ahsoka fans are arguably the worst offenders, however. Padme Amidala has been murdered, driven crazy, subjected to nasty divorces, and outright ignored innumerable times in the name of this ship; it's still bad now, but it was especially bad in the early days of the fandom when Ahsoka didn't have a Love Interest of her own.
Hondo. For some reason, a large portion of the fandom was left puzzled by his willingness to kill children in "A Test of Strength" and "Bound for Rescue", claiming that it was compeletely Out of Character for him. That's despite all the nasty stuff he had pulled in earlier appearances, like threatening farmers with burning down their homes with them locked inside, if they didn't hand over their crop to him. He also very much enjoyed shooting at said villagers with a tank, when they dared try to protect themselves.
After Season 5, Barriss Offee hasn't gotten nearly as much hate as one would suspect. It certainly helps that she was right in her views, though not her actions, and the Jedi Order she opposes already being seen as Lawful Stupid in the eyes of many fans.
Plo Koon was this to supervising director Dave Filoni, and his Ascended Extra role in the series made him one in the eyes of the fans, too.
Cad Bane became one of the most popular characters in the series, as an X Meets Y of Jango Fett and Lee Van Cleef with a cool voice, unusually sinister tendencies, and characteristics of spaghetti-western villains.
Hondo Ohnaka is starting to become one of these. Cranked Up to Eleven in "Revival". And then even more so after "A Necessary Bond." The man snarks at the Sith, how can we not like him?
The mercenary Embo from "Bounty Hunters" was a One-Scene Wonder with acrobatics to make a Jedi jealous, a Nice Hat that serves as a blaster-proof shield and as a Precision-Guided Boomerang. Despite being a relatively minor character in one of the less important episodes of the series, he's popular enough that he got his own action figure and at least one appearance per season afterwards.
Admiral Trench, due to being a clever tactician dangerous enough to necessitate a Jedi-led task force just to defeat him in the series' backstory. His status as one of these is likely what led the writers to bring him back for the post-series stories.
Savage Opress is quite popular too. The fact that he's Darth Maul's brother helps.
The battle droids are so funny that it's really hard to dislike them.
Linked to them are the commando droids, who quickly became popular with fans for being the battle droids only completely fricking badass. Same with the Super Tactical droids, who are like the battle droids only cold, calculating intimidating generals.
A few of the one-arc villains are also quite popular. Riff Tamson and Commander Sobek are two good examples.
Ahsoka and Shaak Ti interacting with each other, with emphasis put on both of them being Togrutas, is a very popular theme.
Fanfics that deal with Ahsoka's future, often include at least one of these elements:
Ahsoka fighting Darth Vader either during Order 66, or years later. These usually go down two ways: either she's killed, or Vader decides to spare her and let her run. Alternate Continuity stories where she kills Vader are practically unheard of.
Ahsoka is in the company of Rex, who decides to disobey Order 66, and warns her to run.
Ahsoka meets with Luke, sometimes because she survived due to one of the options above, 'tho Time Travel and Human Popsicle stories are also common.
Ahsoka and Barriss interacting after Season 5.
Luminara after Season 5.
A lot of these are now pushed onto Star Wars Rebels, especially any involving Ahsoka.
Many fans of the comic books and novels set during the Clone Wars-era declared this on the series.
An interesting variation happened within the series' fandom, regarding the official episode chronology of the anachronically aired first two and a half seasons. Many fans felt that Leland Chee didn't put much effort into it. So when he tried to defend the particularly illogical placement of an episode with an argument that boiled down to him "not paying attention to details", some fans simply decided to ignore his chronology.
Ahsoka/Rex (or Rexsoka, if you wish) remains the most popular Ahsoka pairing, even though she has a canon love interest in the form of Lux Bonteri. This is probably because Lux is comparatively new on the scene and Rexsoka was already well-established in the fandom before his episode premiered in Season 3. Karen Traviss and Karen Miller's teases towards Rexsoka in the novels did not help things.
Asajj Ventress with... pretty much everyone, but special mention goes to Obi-wan where in their first meeting in the show Asajj decides to strip off most of her outfit during her fight with Kenobi. Supplementary materials say that she gets pretty obsessed with Obi-Wan over the course of the war. His retort when she tries to distract him by throwing said clothes in his face? "You'll have to do better than that, my darling." They continue this "flirtation" several more times through out the series, most of their battles double as a flirtatious word war, but it seems Obi-Wan, at least, is being sarcastic, though unlike every other opponent Ventress flirts with, Kenobi is often the one to start it. Then there is their interactions when they work together at the end of season 4.
To an extremely disturbing degree, Darth Maul's psychotic obsession with (revenge on) Obi-Wan. Obi-Wan is the one thing that Maul remembered through his shattered mental state, and in "Revenge", he's heard obsessively muttering Obi-Wan's name over and over again.
Maul: You may have forgotten me, but I will never forget you!
"Funny Aneurysm" Moment: The Season Five arc, featuring a group of insurgents fighting against the Separatists, who Obi-Wan has minor doubts over whether or not their actions may degenerate into terrorism. The capital of this group's home-world is named 'Iziz'. It gets even worse when laterworksconfirm that Saw Gerrera and his group ended becoming one of the more brutal rebel cells fighting against the Empire.
Gateway Series: Like the prequel trilogy, this series served as the introduction for a new generation to the Star Wars universe.
Germans Love David Hasselhoff: Allegedly, the reason why "The Lost Missions" (AKA Season 6) were aired in Germany first (although, the last episodes were released on U.S./Canada Netflix a day before they aired in Germany) is that the series was most successful there. 
Despite complaints on various things, the series has been very well received after season 1 (and a few season 1 episodes are well-liked). The first episode to shuffle that humor aside, and coincidentally one of the more popular episodes, was "Rookies", which introduced the efficient Droid Commandos. Despite the droids eventually losing, it was a step forward in maturity and threat level for the series. The later episode "The Hidden Enemy" is also cited for the same reasons, the droids are more intimidating when using swarming tactics and without the cheap jokes.
"Lair of Grievous" was the first episode to spotlight an obscure Jedi, in this case Kit Fisto. It also builds on why General Grievous is portrayed differently than Star Wars: Clone Wars and re-establishes him as a more complicated character and a very different kind of threat. It ends with an exciting lightsaber duel alongside An Aesop about compromising your values and lusting for power under the pretext of war that becomes more prominent in later seasons.
Season 3's Nightsisters and Mortis arcs.
In Season 4, the Umbara story arc just grew this beard to a whole new level. It does even moreso in the end of that season, when Darth Maul returns.
In the Movie Anakin and Ahsoka rescues Jabba's child. In Return of the Jedi Jabba tries to have Luke (Anakin's son) executed twice, and has Leia (Anakin's daughter) chained to him in practically nothing, which ultimately backfires, when she strangles him with her chains.
Episodes 15-18 of Season 4 are about Obi-Wan going undercover to uncover a Separatist plot against Chancellor Palpatine. On January 26th, the day before the second episode in the arc premiered, Ian Abercrombie (Palpatine's voice actor) passed away. Fortunately the voicework of Season 4 was already done, and so Abercrombie was able to finish voiceovers before he died.
Also, remember the Father's warning to Anakin when he refused? That his selfishness would haunt him and the galaxy at large for refusing to replace the Father? Although at the time the episode was made, they probably were intending to mean the oncoming Jedi Purge, but after the revelation of Abeloth's ties to the Ones in the final book of Fate of the Jedi: Apocalypse, as well as what Abeloth did throughout that series, the Jedi Purge actually seemed not so bad in comparison.
In "The Deserter", Rex states that if the Republic loses the Clone Wars, then "our children and their children could be forced to live under an evil I can't well imagine". Little does Rex know, that such a fate will befall the galaxy when the Republic (or, more accurately the Empire) winsthe Clone Wars, with the galaxy falling under Palpatine's control.
In "Monster", Savage Opress tells Ventress that "so long as I live, you will not harm him!", referring to his brother, Feral. Soon after, Savage was rather brutally proven right: Ventressdidn'tharm Feral. Savage himselfdid.
Ahsoka fighting a brainwashed Barriss in "Brain Invaders" becomes this after the season 5 finale, where Barriss is attacking Ahsoka of her own free will.
Also at the end of the episode Ahsoka wonders whether she should've killed Barriss (who in a moment of clarity, even asked her to do it) because her mercy could've potentially jeopardised the lives of many others. Barriss ends up killing at least seven Jedi, at least two civilians, and injuring many others with bombing the Jedi Temple.
On a similar note, Ahsoka mentioning Clone Sergeant Slick's betrayal to Barriss in the same episode also becomes this when Barriss betrays the Republic and Jedi Order for similar reasons to Slick.
Ahsoka's line in the pilot movie, "I'm a Jedi Knight! Or soon will be." In the season 5 finale, she rejects the possibility of knighthood and leaves the Jedi Order.
In "Clone Cadets", Bravo Squad's line "Time to watch the Dominoes fall" becomes this when you consider the ultimate fate of Domino Squad. Also in the same episode and deliberately invoked at the time of making, Hevy's promise of coming back to 99 for his medal. Considering that the episode was a prequel to the Season 1 episode "Rookies", fans who've watched the episode beforehand know that's not going to happen.
A lot of the series is inevitably going to be this in light of the events of Episode 3. The friendships we see developing between main Jedi characters and various clones makes Order 66 all the more tragic. The Clone Wars Anakin is also a lot more personable and likeable than his movie counterpart, which makes his friendship with Obi-Wan much more believable. This only serves to increase the tragedy of his eventual fall.
In "Weapons Factory", Luminara tells Anakin that she is prepared to let her go of her apprentice Barriss in the event of her death, and asks if Anakin is willing to do the same with Ahsoka. Come "The Wrong Jedi", both of them are forced to let go of their apprentices for reasons that neither of them expected.
Luminara Unduli being held prisoner by reanimated Geonosian warriors in "Legacy of Terror" becomes a lot more disturbing when you consider her fate in Star Wars Rebels.
The opening arc of Season Two becomes much, much harsher in hindsight after Season Two, Episode Eight of Rebels. Here, we see that the Inquisitors kidnap helpless babies with the intent of raising them in the ways of the Dark Side. And this time, the Jedi Order and the Republic aren't around to stop Palpatine's plans.
Ahsoka saves Tarkin in "Citadel Rescue" from being killed at the hands of a Separatist general. Guess what Tarkin would go on to do to Alderaan in A New Hope...
A mind controlled Ahsoka fighting Anakin in "Altar of Mortis" becomes harsher after the Rebels Season 2 finale, when she confronts Darth Vader.
Seeing R2-D2 and C-3PO run out of power and Threepio giving a eulogy-like speech to Artoo in "Nomad Droids" becomes much sadder after Kenny Baker's death.
He's Just Hiding: After "Counterattack", at least one group of fans was convinced that Echo didn't die despite the fact that he was caught in an explosion and we were given a shot of his charred helmet. The post-series spoiler dump along with the Bad Batch arc reels confirm this to be true years later. Echo did indeed survive, but is now a cyborg.
The second episode of MADtv has Gary Anthony Williams doing a parody of Count Dooku (or "Count Poo-Poo"). One year later, he is voicing Riff Tamson, one of Dooku's subordinates, on The Clone Wars.
In the Season 3 Citadel-trilogy Stephen Stanton voiced Captain Tarkin, who was on the run from a Separatist prison, chased by the prison warden Osi Sobeck, a phindian, voiced by James Arnold Taylor. Aiding Tarkin in the escape was Obi-Wan Kenobi, also voiced by James Arnold Taylor. Almost exactly a season later in the Deception-arc, Stephen Stanton voiced Moralo Eval, a phindian on the run from a Republic prison, aided (and secretly thwarted) by Rako Hardeen, who was also voiced by James Arnold Taylor.
Coupled with Actor Allusion, in "The Zillo Beast", there's a scene where Mace Windu is ordering around a clone trooper named Hawkeye. Knowing who Mace was originally played by, and keeping in mind that Marvel's Avengers came out later, and that both properties are owned by Disney now...
In a fanon-example, shipping Anakin/Ahsoka becomes this in the hindsight, that Ahsoka's voice actor, Ashley Eckstein originally auditioned for the role of Padmé.
The "Mortis" arc's high points of this include the first time Qui-Gon Jinn shows up (played byLiam Neeson, no less!)... and the sequence where the Son shows Anakin what he is destined to become. Bonus points for the subtle notes of the Imperial March as a dark cloud in the shape of Darth Vader appears...
Already quite high for the series, it jumps into overdrive any time Darth Maul shows up. For instance:
In "Eminence" and "Shades of Reason", he led a band of Mandalorian warriors and completely owned the Hutts and Black Sun, in addition to taking over all of Mandalore. In previous Expanded Universe works, it's been established that going up against the Hutts or Black Sun (much less both at once) is more or less suicide, which makes it more impressive that Darth Maul took them both down one after another and made them his vassals. In short, no other Star Wars character in the past has accomplished a feat as awesome as what Darth Maul did by defeating the Hutt clans and Black Sun in such a brutal and effective fashion. Granted a lot of those older EU works where the Hutts and Black Sun are practically undefeatable(unless you're Luke, Leia, or Han) are now non-canon thanks to the Disney buyout but it's still pretty impressive how he was able to bring to heel two of the most powerful criminal organizations in the galaxy and take over Boba Fett's planet.
Darth Sidious actually fighting in the following episode, "The Lawless". Darth Maul and Savage always posed a huge menace even individually, and Sidious not only pulls a massive Eviler Than Thou, the series has one-upping an existing feat with the force down in the series, and reduces Darth Maul to begging for mercy.
The good guys in the entirety of the "R2-D2 is lost" 2 parter would have saved R2 and destroyed the listening post with no trouble if it weren't for their insistence on bringing the obviously defective R3-S6 unit along and making it do important tasks that it inevitably screws up over and over again because it's a mole.
The "Children of the Force" mini-arc is based on multiple characters, both good and evil, making errors in judgment.
The second half of "Lightsaber Lost" is ten minutes of Le Parkour which could have been resolved with three seconds of telekinesis. Made all the more apparent due to the multiple uses of telekinesis in the episode itself, just not when it would have caught the lightsaber thief.
The episode "Shadow Warrior", as well, particularly on Grievous' part.
The Gungan General would have lasted about two to three minutes if not for every single character constantly taking leave of their senses. It starts with Hondo deciding to hold Anakin and Obi-Wan for ransom, apparently not realizing that combined with taking Dooku prisoner in any sane universe this would put him on the bad side of both the Separatists and the Republic (not to mention getting on the bad side of three of the most dangerous people in the galaxy). Following this display of insanity Obi-Wan, Anakin and Dooku repeatedly forget that all three of them are powerful force users who could easily get the restraints off or mind control someone to do it for them. It ends with Anakin holding Hondo prisoner, easily able to take him back for trial, only for Obi-Wan telling him to let Hondo go because they have no quarrel with them, apparently forgetting that Hondo kidnapped them, was planning on ransoming them and tortured them when they tried to escape.
The final arc of Season 5, dealing with Barriss Offee framing Ahsoka for bombing the temple. The entire Downer Ending could have been averted if Ahsoka had done a single thing that didn't make her look more guilty, or if the Jedi Council and Republic Senate had bothered even halfway trying to conduct a reasonable investigation.
In general when this series contradicts almost any established Expanded Universe material, it inevitably catches some flack. However the most notable and widespread discontent came from the depiction of the very popular Mandalorians. The Proud Warrior Race was introduced as a planet of pacifists (albeit after a brutal civil war just a few years prior). Now consider some very hardcore fans cried foul over the climate of Ryloth and you can begin to grasp how badly this was greeted online.
Perhaps the worst part of the Mandalore retcon wasn't the switch from militant to pacifist, but the switch from a group which Mandalore the Destroyer described as having "... no species or bloodline ... We're a culture," to planet of pale, platinum-blonde, blue-eyed humans. At one point a Mandalorian academy student identifies a group as "not Mandalorians" because they're "aliens", meaning this isn't just a case of the limited scope of the camera. It is possibly that because of this Internet Backdraft retcons were introduced to harmonize the portrayal of the Mandalorians in the Expanded Universe and the show very quickly in the reference books Star Wars: The Essential Atlas and Star Wars: The Essential Guide to Warfare. Considering the fact that those in charge of continuity had been waiting for the end of the animated series to introduce retcons, this speaks volumes of the Mandalorians' popularity within the fandom, controversial though they may be at times. Of course, these discrepancies (and their fixes) no longer matter anymore, since as of April 25, 2014, the Expanded Universe, which the show isn't considered part of, has been declared non-canon, setting the stage for a whole other Internet Backdraft.
Duchess Satine. In all of her speaking appearances, she's had her closest friends either betray her or die, been almost helpless to stop the corruption and terrorism that threatens her homeworld, nearly assassinated, framed for murder, tortured and been led to believe that Obi-Wan, with whom she's been in love for years, had been killed. It's only the last item on that list that's provoked an openly emotional response, with Satine breaking down in uncontrollable tears. By that point, it's hard to blame her for crying. And in season 5, she is helpless to stop Darth Maul from sowing chaos on Mandalore, and equally helpless to prevent Pre Vizsla from using the chaos to conquer Mandalore and throw Satine herself in prison. To compound this suffering further, Vizsla is then killed by Maul, who pins Vizsla's murder on Satine, near-unanimously turning Satine's people against her, while her world is left to be ruled by a sadistic monster. And finally, in "The Lawless", she is brutally murdered by Maul, who uses her death to torture Obi-Wan.
Savage Opress. He gave himself up to Ventress to protect his brother, Feral, only to be forced to kill Feral while under the Nightsisters' control. And this is after being mutated into a hulking monster by their magicks. Savage then spends the remainder of the Nightsisters arc being trained (read as: tortured) by Dooku, constantly berated by Dooku and Ventress, being thrashed around by two more skilled and experienced warriors, being repeatedly shot by battle droids, and ending up with almost everyone against him with very little hope of being able to fight off all of his enemies. To top it all off, he's still being manipulated by Mother Talzin, and he doesn't even realise it. Even when he's reunited with his only surviving brother, Darth Maul, he's still not treated well and is only used for muscle. His villainous actions may lead to some overlap with Jerkass Woobie. Savage's death only serves to soldify this status. Savage isn't even concerned about his own death; his only regret is that he was an unworthy apprentice to his brother.
Ahsoka. Over the course of the series, she's been beaten, tortured, hunted, nearly killed several times, once literally killed (on an occasion where she was also forcibly turned to the dark side and forced to attack her master), and watched several friends and allies suffer and die over the course of the war. Yet despite all of this, she never complains, never gives up, and never shows any sign of breaking, though there's a Heroic B.S.O.D. or two. It finally catches up to her in "The Wrong Jedi", though, when she leaves the Jedi Order after pretty much everyone save Anakin abandoned or betrayed her when she was framed as a terrorist. Oh, and she's no older than 16.
Asajj Ventress. Even discounting her Dark and Troubled Past, and though she's amoral, vengeance-obsessed, and indiscriminately violent, she's had a rough go of it. Being constantly set up (and brutally berated for) failure by Dooku, betrayed on another Sith's whimsical order, failing to gain retribution for that betrayal, and losing everything she ever worked toward and everyone she cared about in a single stroke. Seeing her break down and beg Mother Talzin not to leave her alone is quite the Tear Jerker.
Dogma becomes one at the end of the Umbara arc.
Boba Fett could possibly count as well. The guy watched his father get decapitated after all.
Darth Maul may be a brutal sadist who slaughters innocent people, but you can't help but feel for him when he's left a broken, psychotic wreck, or when he's helpless to prevent his brother from being killed and he himself is tortured by Darth Sidious. Especially if we remember that he was trained as Sith from birth...
Maul's brother, Savage Oppress, is just as tragic, particularly when he dies.
Barriss Offee. She is a young padawan who is put through several traumas during the course of the war - almost dying, being mind-controlled to the point where she wishes she was dead - only to come to the awful realization that the war is unjust and that the Republic and Jedi Order have become corrupted. While this doesn't excuse her resorting to terrorism to make a point, it certainly makes her more understandable and sympathetic.
Barriss and Ahsoka get a boatload of this in "Brain Invaders". Ahsoka is personally hurt when a brain-worm controlled Barriss attacks her, and cannot bring herself to kill Barriss, despite her pleading to do so (and that Ahsoka had no problem killing with Barriss killing a clone trooper who attacked them earlier). When she manages to lower the ship's temperature enough to kill the worm controlling Barriss, Ahsoka holds her close until they both pass out from the cold, and later, upon waking up, her first words are to ask about Barriss.
They get even more in the season 5 finale arc, where Barriss is the only Jedi Ahsoka feels that she can trust while she is trying to prove her innocence. Later, when Barriss is revealed as the mastermind behind the Temple attack, Ahsoka is clearly crushed by the betrayal. Also Barriss' expression remained as defiant and accusing as her tone was, while she confessed committing the bombing, and she looked everywhere, except towards Ahsoka. Then as she was taken away by the Jedi Guards she finally sends a look towards Ahsoka, and expression seemed genuinely apologetic.
After looking her over and dubbing her "skinny", Bo-Katan slaps Ahsoka on the ass, seemingly just to get a rise out of her.
Riyo and Ahsoka also get a fair bit. It helps that the two are supposed to be long time friends.
Ventress gets some when she fully joins the Nightsisters, thoughit just ends up making her despair at their deaths all the more harsh. When she becomes a Bounty Hunter she strikes up a close (for Bounty Hunters) friendship with Latts Razzi.
Pong Krell is very contemptuous towards the clones serving under him and a massive Smug Snake even before being outed as a villain. Very few will deny that what he did throughout the Umbara arc (especially "Carnage of Krell") was absolutely despicable. However, fans like him as a character both before and after his true colors are revealed precisely because of this, providing not only a good obstacle for the clones from a narrative standpoint, but also demonstrating the corruption of war on the Jedi Order. And his death at the hands of Dogma was incredibly cathartic.
Palpatine's maneuverings during episodes like 'Destroy Malevolence' where he sends Padme on a diplomatic mission that just so happens to lead her right into General Grievous's hands; 'Heroes on Both Sides' where he discovers that Mina Bonteri is responsible for sponsoring the Separatist bill to end the war and her subsequent fate, etc. seem to show that the guy can play the odds and adapt like only a Magnificent Bastard could. Even his seeming mistake in forcing Dooku to turn on Ventress, provokes a protracted struggle between Dooku and Nightsisters, leaving his apprentice busy, weakened and with no one to rely on, so that he's unable to possibly challenge Sidious. Recently, he assures the Jedi that Maul and Savage are "just petty crooks" and that they should focus on the Separatist threat... so he could deal with the Nightbrother duo himself as Darth Sidious. Manages to pull this off again in season 6 when he manages to frame Fives for attempting to assassinate him, fooling everyone into thinking that he had gone insane and convincing even the Jedi that control chips are necessary to keep the clones from going berserk.
Hondo Ohnaka was introduced as this, being clever enough to try and ransom Dooku to the Republic, and then capturing the Jedi sent for him so he could demand more. Even when that went South, he's still kicking seasons later, working for whatever side works best for him, though he's become more Crazy Awesome and less of this trope along the way.
Cad Bane is a master of this from the get-go, managing to successfully take the Galactic senate hostage, break Ziro out of prison, and get away completely scot-free in his first episode. From that point onwards, his plans get crazier and clever as they go on, from disguising himself as a clone trooper and hiding aboard a dropship of actual clones, leading two Jedi masters into a booby-trapped space station, to breaking out of prison again by instigating no less than Boba Fett himself into starting a riot......Every time he appears, he one-ups his previous insane plan, and almost every time, he gets away.
Darth Maul arguably earns the title in "Eminence". Over the course of a single episode, he goes from near-death in the void of space to commanding a veritable army of criminals through little more than words and a careful application of force. He definitively earns the title in "Shades of Reason", successfully concocting a plan that allowed Pre Vizsla to conquer Mandalore with the public's support, then using Vizsla's pride to manipulate him into a duel that ended with Vizsla dead and Maul, as per Mandalorian tradition, as the new leader of Death Watch, and, through a puppet Prime Minister who Maul himself installed, ruler of Mandalore.
Barriss' plan in the season 5 finale qualifies her as one. If it hadn't been for Ventress (and a moment of Bond Villain Stupidity in leaving Ventress alive), Barriss would have gotten away with bombing the Temple while Ahsoka was executed for the crime.
Count Dooku during "Rise of Clovis" and "Crisis At The Heart". He and Darth Sidious are both working on the scheme, but he's the one that carries the plan out and plays Clovis like a flute the whole time.
Memetic Loser: While General Grievous is nowhere near as badass and intimidating as he was in the old series, the fandom/hatedom tends to heavily exaggerate his Badass Decay, by hammering his losses, and overlooking his victories. He has repeatedly proven himself a better swordsman than most of the Jedi he faced, with only Ventress and Kit Fisto actually taking the better of him, without having to resort to using the Force. He has also came out on top in each of his confrontations with Obi-Wan. Despite this, he's "best remembered" by Ahsoka beating him (even though she barely survived the fight), and how he got captured by Gungans (regardless of the sacrifice they had to make to capture him in the first place).
"Memes? We are pirates! We don't even know what that means!"
Sixes. To clarify, in the novel Lords of the Sith, Vader remembers his clone troopers that served with him; Rex, Echo, and... Sixes. Obviously, this was supposed to be Fives, but instead of just putting it down as an error, Wookieepedia created an entire new page for the character 'Sixes' which has caused the fandom to run with it and turn 'Sixes' in to a legendary Memetic Badass who is responsible for many things, such as Grevious' cough and Greedo's death.
An inordinate amount of people seem to think that George Lucas is responsible for any problems with this series. Dave Filoni is the real frontman of the project. To be fair, whole episodes have been written on Lucas' orders, and Dave Filoni has also implied that the show would be rather different if Lucas had not unexpectedly become more involved later in its production.
Likewise, some misblame Filoni or other writers for disregard of certain EU elements, when, by their account, Lucas exercised Executive Veto power.
General Grievous cheerfully shows us what a nice guy he isn't when he orders the Malevolence to target harmless, fleeing escape pods.
When it became clear that he was going to lose Ryloth in "Liberty on Ryloth", Wat Tambor ordered the bombing of every Twi'lek village on the planet - explicitly stating "the inhabited ones first" - just to send the galaxy a message about "the cost of a Republic victory". If he didn't cross it then, he crossed it when he performed inhumane experiments on sentient beings (even killing at least one of them) during the Bad Batch arc.
Cad Bane tortures Jedi to death and kidnaps children.
Asajj Ventress flies past it on hyperdrive, when she goes to recruit an assassin against Count Dooku. Particularly when she tests the brainwashing of the chosen candidate by ordering him to kill his brother. This strikes the viewer even harder, as before that Ventress was almost (sym)pathetic, due to her constant failures. Depending on how you want to look at it it is either a Subversion or a Double Subversion later, as she helps out Obi-Wan and Ahsoka, but asures that she will backstab them whenever it fits her and is still a criminal, just on her own side and not for the Seperatists anymore.
Pong Krell crosses it when he states that Jesse and Fives will be court martialed, found guilty, and executed. Worse still, when Rex tries to argue against it, he just decides to straight-up execute them without trial. He has another candidate for crossing it when he manipulates the clones into killing each other. When confronted on this, he reveals he's actually been a traitor the entire time.
Keeper Agruss makes it clear right off the bat what kind of person he is by dropping several slaves to their deaths just to make a point to Obi-Wan.
Pre Vizsla crossed his by ordering the burning of a village that Death Watch had been terrorizing, simply because they demanded the return of the women he had kidnapped, particularly the chief's daughter. Not only did he burn down the village and kill countless villagers, he started the massacre by returning the chief's daughter, only to stab her in the back immediately afterwards.
Two possible moments for Darth Maul:
Murdering a village full of innocent people, including young children, just to get Obi-Wan's attention.
Darth Maul: With the galaxy at war, Savage, there is only one way to draw the attention of the Jedi: slaughter of the innocent. Mercilessly, and without compromise.
His callous, brutal murder of Duchess Satine, done only to torture Obi-Wan. Not just the act itself, but the sadistic pleasure he takes in Obi-Wan's suffering.
Lok Durd crosses this when he threatens to torture Ban'tena Fhernan's family to death if she commits suicide instead of helping him.
Barriss crosses hers by arranging a bombing of the Jedi Temple, then killing the pawn she used to orchestrate it and framing Ahsoka (her friend) for those crimes and more, which nearly resulted in Ahsoka being sentenced to death.
If placing mind-control chips in all the clones wasn't atrocious enough, Kaminoan scientist Dr. Nala Se may have crossed it when she attempted to have Tup euthanized for having Order 66 prematurely triggered (something beyond his control) and then threatening to have AZI-3 and Fives decommissioned for coming close to discovering the truth. If not that, her alternative MEH may have been when she drugged Fives on the trip to Coruscant, causing him to become paranoid and ultimately resulting in his death at the hands of his own brothers. In the end, the truth about the "inhibitor chips" is covered up with a claim of a rare parasite, Order 66 remains undiscovered by the Jedi and Nala Se gets off scot-free.
Ganodi's disproportionate breakdown in "The Gathering" when confronted with a large number of crystals, especially since she was previously whining about not being able to find any crystals. Now she's whining about there being too many.
Savage giving a panther roar in "Eminence". For that matter, just the fact that he's named "Savage Opress" could qualify.
On a similar note, Darth Maul growling like he's some sort of dog in the same arc.
Satine's nephew's name is Korkie. It's hard to explain, but that name just cannot be taken seriously.
Yoda's vision of Ahsoka dying. They're on the corridors of the Jedi Temple, surrounded by the corpses of several Jedi, including Windu and Petro. Ahsoka is writhing on the floor, and asks Yoda for help actually saying that she's dying. Yoda then starts tottering like he's about to collapse, crying that he had failed the Jedi Order. While the scene is definitely meant to be taken seriously, due to the laughable lines, and their overly hammy delivery by Tom Kane and Ashley Eckstein, it comes off as incredibly corny.
Almost everything Hondo does, presumably because he does it with such gusto that you can't help but like it. Especially his acting when using a Motivational Lie to get Katooni to finish her lightsaber before going into battle. It's so over the top and over-acted, but instead of Narm it's a Crowning Moment of Heartwarming.
The very first time Ahsoka met Cad Bane, he electrocuted her twice -first to knock her out, then just for the fun of it- and handcuffed her, with shackles that hurt the more you struggle. Then he caressed her head in a rather creepy manner, before taking her Padawan Braid as a trophy. Much later, when Ahsoka protected an unconscious Anakin from him, he left, promising her a dance at another time.
The way Garnac, the leader of a Trandoshan hunting party acted towards her. If the whole kidnapping Jedi children to hunt them down thing wasn't clear enough, he provides lines like these:
Garnac: She (Ahsoka) can't hide forever! Mark my words, I'll have her skin and nail it to the wall for killing my son! Garnac: A valiant effort, little younglings. Especially you, Togruta. You'll be a prized trophy for my collection.
Older Than They Think: The entire concept of a cyborg Darth Maul was originally used in the non-canon comic Star Wars: Visionaries. The character's initial appearances (up until getting a redesign in the fifth season) are directly based on his portrayal in said comic.
Liam Neeson reprising his role as Qui-Gon Jinn in "Overlords", "Ghosts of Mortis" (for one scene each), and "Voices".
The appearance of the characters from Star Wars: Republic Commando (Boss, Scorch and the rest of the Clone Commando squad) in the third season episode "Witches of the Mist".
In "Sacrifice", Darth Bane's appearance, being voiced by Mark Hamill.
Padding: The Season 5 episode "A Sunny Day in the Void" is perhaps the most uneventful episode of the entire series, consisting almost entirely of D-Squad, Colonel Gascon and WAC-47 wandering around the desert planet Abafar for 22 minutes. The only reason it seems to exist is as character development for two characters whom nobody really liked, and it's not hard to imagine how it could have been made more interesting or replaced entirely with an episode that was more exciting.
Pandering to the Base: David Filoni acknowledged the negative reaction from the first half of the third season (which was focused on heavily on politics, trade blockades, bank interests, and stuff like that) and said that the amount of such episodes will be severely cut down.
Popularity Polynomial: Fans hated The Movie upon its release, but the fans that enjoy the show have since warmed up to it after the show itself started airing. The dislike of the movie most likely came from the fact that it wasn't an "actual" Star Wars movie, but an ad for a television series - and, when taken as four episodes tied together instead of a movie, it works more effectively.
Jar Jar Binks. Yeah, you read that correctly, no mistake - they successfully rescued Jar Jar Binks from the scrappy heap. They did so by emphasizing his friendliness as being his greatest strength, to the point of being The Beast Master, once calling upon a giant swamp creature for help. They also played down his clumsy side making sure that it always ended up doing more good than harm, and he gets to show that under his overly friendly and clumsy nature is indeed a smart guy who takes his duties seriously. His cowardly nature is also almost nowhere to be seen. His most highly-regarded episodes are those where he's paired up with another character to act as a counterpart to his wackiness (such as C-3PO, Bail Organa, and Mace Windu). While there is still some vitriol directed towards him for his reputation in the films, the reception to him here is significantly less caustic, making him more of a Base-Breaking Character than the near-universally-loathed Scrappy he once was.
Also, Anakin. Originally a Base-Breaking Character in the movies, he's far more unanimously liked in the series due to his stronger characterization, his decreased tendency for Wangst, and Matt Lanter's voice acting being more well-received than Hayden Christensen's acting. It helps that the show constantly proves that Anakin will do anything to protect those he cares about and to bring peace to the galaxy, making his fall a lot more believable than what was presented in the movies.
Ahsoka started out with similar levels of hatred to Jar Jar Binks, mostly for her being perceived as the Spotlight-Stealing Squad. Fan reaction became more positive after Season 2, after pulling back from having her in nearly every episode, also preventing her from being one of the more talkative characters in the series. With several well regarded episodes highlighting her own personal growth and the emotional response to her leaving her master and the Jedi Order, it's safe to say that her "Scrappy" status has been revoked.
As of season four, arguably the entire Gungan race as well. In the episode "Shadow Warrior", they take down General Grievous, albeit only when Captain Tarpals pulls a Heroic Sacrifice, successfully incapacitating him and allowing him to be captured.
After the season 5 finale, the Council and especially Windu tended to get a larger chunk of blame from the fans for Ahsoka leaving the Order, than the person who orchestrated the bombing of the Temple and framed Ahsoka for it, simply because she made a good point about the Jedi losing their way in the war, and because Windu made a rather insensitive comment. Curiously, some fans actually feel like the writers themselves have done this to the Jedi in the series.
Lux Bonteri. People seem to hate him for no reason other than he is a heterosexual love interest for Ahsoka, even going so far as to defend Barriss' horrible actions in The Wrong Jedi and exaggerating his flaws to make the option that Ahsoka is gay look more appealing.
WAC-47 and Colonel Gascon were this for the D-squad arc, with some people finding the duo so annoying that they even made comparisons to Jar Jar Binks.
Lieutenant Tan Divo, due to him being both irritating and largely incompetent. He is also this in-universe; no one seems to like or trust him, and each time he appears, the characters choose to take matters into their own hands rather than letting him handle it.
In-Universe example: After R2-D2 is lost in battle, Anakin is distraught over losing a friend, while Obi-Wan dismisses R2 as a "dime-a-dozen" droid. Ahsoka gets Anakin a new droid, R3-S6 ("Goldie"), who seems vastly inferior. And in the end R3 turns out to be The Mole.
Pong Krell serves as one both in-universe and out in the Umbara arc. The promos even outright say that Krell's not as cool as Anakin
Self-Fanservice: It's not like Ahsoka's canon outfits didn't easily qualify her for Ms. Fanservice, but around half of the fanart of her on Deviantart, depicts her either in even less clothing, and/or with a significantly larger bust, or at least in rather compromising poses. The same goes for Ventress and Aayla.
So Cool, It's Awesome: Apart from the contested movie and a large portion of the first season, the series is highly regarded by Star Wars fans, just like the microseries, and is widely praised for its storytelling and willingness to take darker turns. You'd be hard-pressed to find a fan with more complaints about The Clone Wars (again, except for the first season) than any of the prequels.
In Corruption, Duchess Satine of Mandalore is shocked to discover just how far corruption has spread throughout her government. When she, Padme and her guards manage to find and apprehend smugglers bringing in tea which they have diluted with toxic chemicals, she orders the entire facility burned to the ground. The commander of the police protests that there is evidence in the building, but Satine explains that if he does not comply she will consider him a co-conspirator with the smugglers and then she goes off to find out just how high this conspiracy reaches. His initial disinterest in investigating her accusations certainly was suspicious, but by ignoring his advice and burning down the building Satine has eliminated any chance of finding records or documentation listing who was involved in the smuggling program, physical evidence placing people at the scene, etc. For a person who claims she is interested in following the web back to its source, Satine ignores rather legitimate points about proper criminal investigations.
In "Heroes on Both Sides" the message of the episode appears to be that not all of the Separatists are evil and in fact, most of the Separatist people are not. Just the various leaders and villains of the week that show up from time to time. Anakin is clearly shown to not agree with this, viewing all of the Separatists as wrong at best and evil at worst. The problem with writing him off as the narrow-minded one though is that the only remotely decent Separatist characters we ever meet are the Bonteris and Bec Lawise. And Mina Bonteri and Lawise are both later killed by the man they openly admired, Count Dooku, and the death of the former prompts her son, Lux to abandon the Separatists. Between this and all later named Separatist characters also being evil, it becomes a lot harder to disagree with Anakin's viewpoint.
Tee Watt Kaa, the leader of the Lurmen in "Defenders of Peace", is a pacifist and wants his people to remain neutral in the Clone Wars. Unsurprisingly, the Separatists attack, and Tee Watt Kaa is portrayed as a Stupid NeutralExtreme Doormat... except for the fact that he was absolutely right that remaining neutral should have kept his people out of the war, and was only "disproven" because the Separatists attacked his people to test a weapon.
Squick: Filoni self-admittedly put together at least two couples, who'd the average viewer would never want to see making-out, just for the sake of getting this reaction:
Ziro the Hutt, a purple, Camp Straight giant-slug with a toad-like face, and Sy Snootles a Pal'owick, a long-limbed frog, with a humanoid feminine lips at the end of a stalk are shown kissing on close-up.
When questioned by Windu, about where he had been all night during their mission to Bardotta, Jar Jar loudly and proudly admitted that he was "loving Queenie Julia".
Take That: This series' depiction of the Mandalorians — a once-brutal, war-like culture who so devastated their own planet with internecine conflict that, eventually, the downtrodden non-Warrior castes rose up, exiled their warriors to the moon to die out on their own, and painstakingly rebuilt their planet whilst embracing a philosophy of pacifism — seems almost to have been made to give a great big middle finger to the depiction of Mandalorians favored by Karen Traviss.
Take That, Scrappy!: While Jar Jar was Rescued from the Scrappy Heap in this series, some of his rescuing comes at his own expense. For instance, some of the people who don't know him as well are wary of working with him, suggesting they keep him out of some more delicate political matters and let someone more experienced handle the situation. On another occasion, Obi-Wan suggested Jar Jar be trained to use a blaster, with Captain Rex bluntly telling him he's not going to the one training him.
Count Dooku, although not underused or ineffectual by any means, wasn't especially fleshed out apart from his role as a villain. His "political idealist" nature, described from the films, remains an Informed Attribute, and despite his position as The Heavy for the series, we learn little about him as a character that we didn't already know from the films. "Nightsisters" and "Monster" both show some signs of giving Dooku some Character Development, but after that, he remains fairly one-dimensional.
Upon the return of Darth Maul, Savage Opress is relegated to being Maul's muscle. His Noble Demon traits from before his transformation in "Monster" are also severely toned down until his death.
Several of Grievous' appearances in season 1 imply a degree of friction between him and Dooku, with Grievous' track record and frustration with his incompetent troops being particular points of contention. This never goes anywhere, and Grievous never shows any sign of discontent towards Dooku again. While Grievous must remain Dooku's general until they both die in Revenge of the Sith, the writers missed out on some prime Character Development for two of the show's biggestvillains.
Similar to the above, Dooku suggests in season 3 that he plans to betray Sidious and become the new Dark Lord of the Sith. After Savage leaves Dooku's service, this storyline is never mentioned again, with Dooku spending the remainder of the series as Sidious' loyal subordinate. Again, while Dooku remaining Sidious' apprentice is a Foregone Conclusion, it's still a lot of wasted story potential. Though What Could Have Been before the series cancelation would have gotten to the Dark Disciple arc, which is now a novel, and does allude to Dooku's intended betrayal.
Luminara Unduli is completely absent from the season 5 finale, which includes the revelation that her apprentice has become a Knight Templar terrorist responsible for bombings against the Jedi Order, making her exclusion rather glaring.
In an aversion of this, Embo was originally going to be this in his debut episode, "Bounty Hunters". He ended up being popular enough with the production crew (and the fans, afterward) that he was re-written to have survived the episode and then make at least one cameo per season.
A lot of people who liked the original Clone Wars series were worried that this would be inferior, and debates on the matter still can get heated. Fans of the old series often complain about TCW's lack of a cohesive narrative, Grievous not being badass enough, and lots of wasted potential, while fans of TCW claiming that the Genndy-series was ridiculously over-the-top, and that it didn't offer much story, and Character Development wise.
In turn the Star Wars Rebels, is already getting some fire from fans for replacing The Clone Wars, mostly due to fears that Disney won't allow the show to get nearly as dark and brutal as The Clone Wars could get sometimes. After the end of its first season most of these fears have been elevated, especially after the reveal of Ahsoka as Fulcrum, and the show is starting to be considered a worthy successor.
Ugly Cute: Embo's pet anooba, Marrok. Anoobas are vicious hyena-wolf creatures capable of tearing a man's throat out, but Marrok is like a puppy when he is not fighting. His more adorable side is best shown in "An Old Friend", where he can be seen giving Embo a sentry droid like he's wanting to play fetch or retrieving his hat when he loses it.
Uncanny Valley: Though most of the characters look exaggerated enough to not really fall here, Riyo Chuchi in the "Trespass" episode, when she is looking head on into the camera and speaking, you kind of have to do a double take.
Unpopular Popular Character: In universe, Hondo Ohnaka isn't exactly the most popular character. Both Sith and Separatists hate him for either capturing their leaders or humiliating them in some way. He's not too popular with the Jedi either and even Obi-Wan, the one Jedi Knight whom Hondo considers his friend, sees having to deal with Hondo as an unpleasant chore. He can be popular with his own men but even they would willingly backstab him if they saw an opening, since they're all space pirates. With fans, however, Hondo is wildly popular as a Breakout Character and even now, there are some people petitioning for him to be included in the new Star Wars movies.
Villain Decay: General Grievous in early episodes was close to losing nearly every battle and retreated before his ship or outpost was destroyed. Acknowledged In-Universe with "Lair of Grievous", where Dooku is unhappy with Grievous' decay and sets out to test him.
"Grievous Intrigue" and later episodes, however, try to find a compromise of sorts; Grievous remains a nasty, menacing villain and a legitimate threat, but still runs when he feels that he's on the losing side, and more of his menace comes from his being a Chessmaster rather than a full-on badass like in the 2003 series.
For some he completely reverts any remaining Villain Decay in "Massacre" through the duel with Ventress and extermination of the Nightsisters and for others it was just cringeworthy to see him lose in a lightsaber duel again which only didn´t go south because of his army and because total victory depended more on the Defoliator tank than any of Grievous´ strategy.
Some of the episodes written by Christian Taylor that explore the nature of the Force (the Mortis trilogy, "The Gathering" and the Yoda arc minus "The Lost One") can be very surreal even by Star Warsstandards to say the least.
Season 4's droids two-parter ("Mercy Mission" and "Nomad Droids"), while more light-hearted than Christian Taylor's episodes above, is also pretty out there. The first part has the droids travel into an alien underworld with sentient trees and magical blood-sucking nymph. "Nomad Droids" takes it even further on the merit of the droids going from one bizarre misadventure to another in the span of a 22-minute episode. These misadventures include fleeing from a space battle with little context to being kidnapped by Lilliputians and accidentally overthrowing their despotic leader to then being kidnapped by a cult enslaved by pit droids behind the scenes to being salvaged by Space Pirates to participate in droid cockfights before eventually being reunited with the Republic during another space battle with little context, referencing many well-known stories in the process. The 1980s Droids cartoon, which these episodes were taking inspiration from, was also just as bizarre.
What Do You Mean, It's Not Political?: Many of the "deeper" episodes dealing with the political and economic realities of the Clone Wars contain what many consider to be increasingly-thinly-veiled commentary about the political situation in America at the time (mostly the Bush Jr. Administration and wars in Afghanistan and Iraq.) This likely contributed to the backlash and Pandering to the Base that saw such episodes all but vanish from the series after Season 3.
Win Back the Crowd: Did so for people who were critical of (or outrighted hated) the Prequel era, or anything made with George Lucas' involvement for that matter. With some Original Trilogy fans who didn't like the Prequels even going so far to say that this series is what the Prequels should have been like.
The Woobie: This series is not kind to its characters, to say the least.
The three Jedi younglings in "Padawan Lost"/"Wookiee Hunt", who had been relentlessly hunted by the Trandoshans to the point where they had all crossed the Despair Event Horizon by the time Ahsoka arrived. Special mention goes to Kalifa, who struggles to keep the other two younglings safe, and is the only one who doesn't get off Wasskah alive.
The clone troopers:
The entire Umbara arc. They spend the entire arc being abused by Krell, watching clone after clone die from his pointlessly reckless tactics, and being manipulated by Krell into killing their own brothers. Rex, in particular, stands out, especially when he realises exactlywho he and his men have been shooting at.
Waxer's death scene sets him up as, arguably, the biggest woobie out of all the clones in the Umbara episodes.
Fives. Apart from experiencing everything the other clones did, he was almost executed, and before the Umbara arc he had to cope with the other members of Domino Squad being killed off. It only gets worse for him in the Order 66 arc, where he discovers the order and eventually gets killed for it.
The Togruta colonists who were abducted and enslaved by the Zygerrians.
The Father. After spending God knows how long keeping his children in check (and having to live with the fact that they, as he says, could tear apart the fabric of the universe), his only reward is to be dying by the time the Jedi arrive on Mortis, as well as nearly being murdered by his own son, watching his daughter sacrifice herself to save him, and having to arrange his son's death before dying of a self-inflicted stab wound.
The Son, ofallpeople ends up as one by the end of the Mortis arc. Despite his nature, he did still care for his family. He is horrified and so heartbroken by The Sister's death, and even the death of The Father that it's hard not to shed a tear for him.
Less so than in the films, but Anakin still qualifies, especially in the Mortis trilogy and the season 5 finale. In the former, he's confronted by the truths of his destiny, emotionally manipulated by the Son, forced to duel Ahsoka, and Mind Raped into turning to the dark side. In the latter, Anakin does everything he can to help Ahsoka, but is powerless to clear her good name until it's very nearly too late, and still loses his beloved Padawan when she leaves the Jedi Order.
Rush Clovis during "Rise of Clovis" and "Crisis at the Heart". Given a chance to do good by taking a chance to lead the Banking Clan, but his taking the position was just to turn him into an Unwitting Pawn of Dooku and Sidious, ends up bringing the war to Scipio and he watches everything fall apart around him. In the end, he sacrifices himself (possibly out of guilt for his actions) to save Padme's life, and to pour more salt in the wound, he gets scapegoated for the corruption in the Banking Clan and control of the banks falls into the hands of Palpatine.
Simon Pegg being the voice of Dengar in the season 4 episode "Bounty" raised the eyebrows of fans due to his frequent criticism of the prequel trilogy and the Special Edition and Blu-Ray versions of the original trilogy, and he takes every opportunity he can to bash anything Star Wars post-1983, even the people who like them. Some hated that he'd be allowed to be involved in the franchise, while others found satisfaction that die hard prequel detractor Simon Pegg found that the series (or at least his role) lived up to his standards of Star Wars.
The mysterious BJ Hughes temporarily voicing Jar Jar Binks before Ahmed Best returned.