These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Sentinel Prime suffered severe psychological damage in the incident where Elita-1 was lost. Since then, rabid fear of organics and guilt over leaving Elita-1 to die have been gnawing away at his neural nets, turning him into a paranoid wreck who's convinced he's the Only Sane Man. Or just some self-centered jerk who just won't take responsibilities for his actions. A slight riff on the former: Sentinel and Elita-One were romantically involved (you see his arm around her waist and he puts in every effort he can to protect her, even covering her and Optimus' retreat. When she fell to her 'death,' he's willing to throw himself into a damn inferno to save her.) Yeah, he took her death pretty hard, especially since his and Optimus' rule-breaking (going to that off-limits planet) caused Elita's death. Now, in the present, he's convinced that rule-breaking will always cause heartbreak. That's why he's so obsessed with regulations and order, to keep others from suffering that same loss. He wants to do good in that regard, but he does need a little guidance; after you realize that, it's hard to hate him. Alternate Character Interpretation, indeed.
Invoked with Blackarachnia's last scene. Waspinator was destabilizing due to the Transwarp energy she infused him with, and was close to exploding. Blackarachnia encased both herself and him in web, lessening the explosion. Optimus says she did that to save them, sacrificing herself, Sentinel says she did it to harness the energy and teleport out, sacrificing Wasp.
Adaptation Distillation - Most notable is in the character of Starscream, who makes his first bid for leadership in the first episode. He is very literally the distilled character of G1, who took until the movie when Megatron was injured from a battle with Prime. Here he is much more proactive, planting a bomb on Megatron before he goes off to fight the Autobots.
Badass Decay - The Dinobots, to the point where they were easily beaten by Jetfire and Jetstorm and scared off by post-upgrade Sari by Season 3. Oh, and according to Grimlock's profile, he's as powerful as Megatron.
Most of the Decepticons suffer from this. Blitzwing and Lugnut are the worst cases, they are shown to able to beat all five of the main autobots on their own, and since the Autobots getting their asses kicked all the time would get old, beating them has to constantly require the use of plot devices that render both villains to Butt Monkeys
Blackout suffers this in the Cool comic, where Jetfire and Jetstorm dodge his attacks, and combine to take him down. Blackout killed 3 bots the size of Omega Supreme in the war by himself, and lead a bombing raid against a fourth, and he seems to forget that he's covered in weapons.
The reveal of The Motor Master's design met with some contention. There were fans of the design, using the Voyager Optimus Prime gave him a beefy Evil Counterpart appearance. There was also a number of fans who didn't like the design, some felt that the blocky head clashed with the more curved design of the body, with those fans feeling the use of the Wreck Gar mode to be more suitable. Finally other fans feel that complaint applies more to the character model rather than the toy.
Broken Base - For every dozen or so Transfan that adores the show with full heart, there is usually one that dislikes it with as much hate as their love combined. This being the Transformers fandom, this is unsurprising.
Lockdown killed his old master (as well as The Obi-Wan to Prowl and Jazz) to steal Transformer infants protoforms in order to sell them and tortures his bounty hunting victims by cutting off their specific upgrades and using them to make himself more powerful. He enjoys hunting more for the thrill of the chase and the chance to vivisect his victims than anything else.
Another true monster is the human supervillain Meltdown. After being mutated by his own experiments, he tries to kill his rival, Isaac Sumdac, in a fit of rage whilst blaming him for all his problems (including his self-inflicted transformation). Later, he becomes so obsessed with creating a human transformer, he not only mutates at least two innocent humans into gruesome hybrids mish mashed with animal parts, he decides to kidnap Sumdac's innocent eight-year-old daughter as his newest test subject (deciding to experiment on children in general now). When Blackarachnia breaks him out of jail in exchange for him eliminating her organic half, he double-crosses her and tries to destroy her transformer half - a deed which, if not destroying her soul completely, would have left her with a completely organic body she's disgusted with. But damn, can he dance. He also forces the Dinobots to work for him by painfully burning them with his acidic touch until they follow his commands. He hurt them so badly, that they were willing to turn on Bulkhead and Prowl, their only friends among the main cast, just to stay in Meltdown's good graces. No wonder Meltdown is the only human villain in Animated played as a deadly serious threat to the Transformers. Dancing aside.
Damsel Scrappy: Sentinel Prime is an unusual male (not to mention giant alien robot) example. Most of his time onscreen involves him getting into some scrape or another and having the long-suffering Optimus get him out. It seems the only thing that keeps Optimus from abandoning him is a sense of guilt about their shared past and perhaps some level of fondness for his old Academy-mate.
Mix of all of the above, and the hope that Sentinel gets it through his thick head that his arrogance is a Bad Thing. But Status Quo Is God and he always rubber bands back to being a jackass by his next appearance. Even Jazz, who has long tolerated (or ignored) it as his second in command, finally gives up and more or less defects to Prime's crew.
Designated Villain: Played With for Prowl in "Five Servos of Doom." He's supposed to be an undisciplined Maverick who learns to be more humble and fight for a good cause under Yoketron, but the reason he's brought to Yoketron in the first place is because he's a draft-dodger. Prowl states he doesn't want to fight in the war, and he's shown to have been rounded up and forced to participate. Warpath, the arresting officer even threatens to take him outside and beat him up until he agrees. In essence, he was pressed into service, and villainized for not wanting to go out and risk death for the people forcing him into the war. On the other hand, the Decepticon threat was so great that the Autobots were reaching Godzilla complex, what with Project Omega, and were forced to make certain moral concessions, so the Decepticons don't win, and make life even worse for people under their oppression. Forced Military service was just one of these moral concessions, all for the greater good.
Surprisingly, Sentinel Prime is also popular amongst the fans. Partly due to his Love to Hate status, and partly due to it being hilarious seeing him get his skidplate handed to him regularly. Even so, some fans just outright hate him, making him a bit of a Base Breaker.
Captain Fanzone is also pretty well-loved by the fans.
Amongst the non-Decepticon villains, Meltdown seems to be the most popular due to being a terrifying Knight of Cerebus who can actually hold his own against the Autobots rather than being a joke villain like Angry Archer or Professor Princess. And he can dance!
Fanon Dis Continuity - Some fans still refuse to acknowledge this version exists, their main complaint being the art style.
Others love the first two seasons but despise the third because of the tone shift from fun and happy to Anyone Can Die.
And of course, there is even a flip side to this opinion as well, with certain fans who weren't as fond of the show suddenly becoming hooked after viewing the third season and its more serious attitude.
Freud Was Right: In "Three's a Crowd" we see that in robot mode the neck of Scrapper's power shovel comes out of his crotch.
God-Mode Sue: Jetfire and Jetstorm. In addition to being Autobots with flight and jet-modes, they can actually fly FASTER than the Decepticons and due to their Super Power Lottery, out-gun most of the characters and can combine into a stronger robot. Even when confronted by Blitzwing, Lugnut, and two of Starsceam's clones they still only lose because of Blitzwing using Sentinel Prime as a shield.
Growing the Beard - "Thrill of the Hunt" was a strong and mature episode that addresses consequences and regrets during war time and won over the fans who thought this series was just going to be slap-stick comedy.
One of TF Wiki's earlier image captions for Lugnut describes him in relation to Shockwave and Omega Supreme. This becomes amusing when Animated Shockwave is introduced and Lugnut feuds with him on who is Megatron's most loyal servant. And then the last episodes have the creation of Lugnut Supreme, based on Omega Supreme, which involved both Lugnut and Shockwave.
Hollywood Homely - Blackarachnia, at first. She's supposed to be hideous due her techno-organic status, but both to the viewer and most of the Autobots she's a beautiful Femme Fatale. And then her helmet comes off and this trope is subverted so fast its head spins.
HSQ: The ending of season 2 and the first few episodes of season 3.
Magnificent Bastard: Megatron, Soundwave, and Meltdown. Starscream tries to be this, and is definitely more successful than most incarnations of the character, but ultimately he's just too egotistical and Stupid Evil.
Memetic Mutation: Shockwave's difficult to hear and completely out-of-character "LIAR! LYING LIAR!" has become a bit of an in-joke amongst his fans.
Moral Event Horizon - In "Predacons Rising" when Waspinator told Bumblebee that Wasp forgives him for getting him sent to the stockades followed by "But Waspinator never forgive!"
Prometheus Black decides to use the child of his "arch-nemesis" as the test subject for making an organic Transformer. This is after he already tried it on two adults and permanently left them in misshapen bestial forms.
Most Wonderful Sound - This is the first time the Autobots themselves have mentioned the iconic transforming noise. When the Bots are trying to will themselves back to their normal states in Soundwave's Lotus-Eater Machine, Bumblebee suggests that Bulkhead make the noise with his mouth.
Narm Charm: The series' approach to combining humour with drama makes the whole thing remarkably cheesy, but there's something inherently lovable about the way much of the main cast (and that includes many of the villains) are nobodies, screw-ups, and nutjobs.
Robotic Reveal - Sari injures her elbow at the end of the second season...revealing Cybertronian circuitry within.
Which also makes this a bit of a We Knew It, as several fans already suspected it, between having no identity papers and no obvious mother while her father was a robotics expert.
Ironically, it was her father who accidentally turned her human, although Sari did assume at first that he built her. Sari's unfinished protoform absorbed humanity when Sumdac reached out to touch her. Good thing Blackarachnia never found out...
While they did help stave off Villain Decay and Menace Decay for the Decepticons, the human villains are generally disliked for being gimmicky and taking screentime away from the Transformer vs. Transformer conflicts. The sole exception seems to be Meltdown, since he's actually dangerous to the Autobots and serves as a menacing villain in his own right. Technically speaking though, he's not human-at least not anymore.
Squick - Captain Fanzone dangling a loogie towards Rattletrap, and sucking it back in when the latter telling him what he wants. Excuse me for a sec....
Strawman Has a Point: In "Predacons Rising", Sentinel discovers Blackarachnia's true identity Elita-1 and that she has just transformed Wasp into Waspinator via her transwarp chamber (he was manipulated into it). Despite the former revelation, Sentinel, being an organic-phobe, is actually willing to kill Blackarachnia, to put an end to all this. While his approach to the situation is most certainly wrong, given how she hasn't actually harmed him yet, he does have something of a good point in this line below, given what she's just done to Wasp:
"Don't say that name! You don't deserve to say that name! You're not Elita-1, you mutant freak. Elita-1 went off-line a long time ago."
Take That, Scrappy!: Rodimus Prime, in his first appearance he ends up getting afflicted with cosmic rust. This has satisfied some fans who don't like Rody.
They Changed It, Now It Sucks - When Takara Tomy announced that they were tying Animated (well, their handling of the show) with the movie-verse, change in episode order and renaming Bulkhead to Ironhide (even though there was already an "Ironhide")... Well...it sure did help that the Japanese dub didn't turn out to have any major tie-ins with the movie-verse at all and had some awesome music by Jam Project. What actually ended up going on: change in episode order and Ironhide rename still happened, fans were also annoyed by cuts to the episodes made in favor of live action segments featuring the Ototbotto family. There were also various instances of Cultural Translation and some characterization changes made, like Bulkhe—uh, Ironhidebecoming more of a simpleton than the original Bulkhead and Bayformer Ironhide ever were.
To say that some fans were not pleased when it was revealed that in this show's universe Optimus was not the Big Good of the Autobots but just a low level commander would be the understatement of the decade.
They Wasted a Perfectly Good Character: Team Athenia and Team Chaar open out season 3 with an epic battle, and never appear again, outside of cameos. This is especially egregious because they got considerable hype, appearing prominently in the transwarped debut trailer, and even had profiles published in the Magazine before the season aired. Perhaps they will do more in the comics.
Likewise, Blackarachnia in the Megatron Rising two-parter. All her appearance amounted to was creating a continuity error (e.g, she wanted to be fully mechanical again, which is what she already tried doing in her formal debut, but it wound up almost killing her; unlessthat's what she wants) and getting Sari to the Autobots faster to help them. One wonders if she was forced into those episodes.
They Wasted a Perfectly Good Plot - This is arguably what happened to Sari's upgrade, and her backstory in general. We never see the immediate fallout of her upgrade and near-overload, since she vanishes for four episodes afterwards, and we never find out how she got to Earth in the first place.
Blame Executive Meddling for that, they demanded that the human characters be shoved to the background to focus on the characters with toys for the third season, including Sari.
There are a lot of great plot threads that are still left hanging by the end; Wasp becoming Waspinator and Elita-1 having become Blackarachnia; the former could have allowed for some great character development from Bumblebee and the potential for him to mature.
The Woobie - Part of the reason Sari has avoided becoming The Scrappy is because her life sucks so much. (Come Season 2, anyway. Omega Supreme can't seem to catch a break either, and Ratchet's had it nearly as bad.)
Blurr instantly became this when he was killed by Shockwave in the season three premiere, as mentioned above.
Optimus Prime's backstory involving Elita-One.
Rachet, considering what happened to him involving him, Arcee, and Lockdown
He barely catches a break in any of his appearances.
Arcee has been one in her every appearance.
Skywarp, and his predecessor, #3370318. Poor guys; life is scary!
Bulkhead has his Woobie moments too.
Then there's Wreck-Gar. He was a newly-activated Transformer with no sense of identity. Then comes Rachet's jerkassness. After wiping nanobots of a boat they were on, the last thing he says to Rachet before he seemingly explodes were "Thank you!". Luckily for the viewers, he survives.