* AccidentalAesop: Going through the book's history, it seems that many of the problems could've been avoided had certain people learned to live and work better with others, understood that their value systems need to change overtime, or just let go of their grudges with certain characters. Sally follows this when she talks to the Prowers and forms the council, but many of the councilors didn't let go of their grudges with the royal family or Freedom Fighters.
* AccidentalInnuendo: Almost certainly unintentional, but still: Lupe comes from the word ''Lupa'', which is Latin and means either ''she-wolf'', or, well...
* AlasPoorScrappy: [[spoiler:Tommy Turtle.]]
* ArcFatigue: It's generally agreed that "Iron Dominion" overstayed it's welcome. Some are willing to forgive for setting up the epic "Genesis" story arc, but this is far from universal.
* ArchivePanic: It can be hard to get into the comic at first because of it's vast, complex backstory developed over 200 issues, any one of which can be referenced at random in a newer issue.
** Though thanks to the retcon, it provides a good jumping on point without having to worry too much about history. Though how long that lasts...
* AuthorsSavingThrow: Ian Flynn's fans believe he has managed to pull off a lot of these, especially regarding plots left dangling or satisfied unsatisfactorily by the previous author.
** A few also see the post-''ComicBook/SonicTheHedgehogMegaManWorldsCollide'' issues this as well, essentially saving a comic that had many of its characters and lore ripped out by flip-flopping the focus from [=SatAM=] material to Sega material and a lawsuit from an embittered ex-writer.
* BadassDecay: [[TheDragon Metal Sonic]] gets hit with this hard in this series; he is much less powerful than in other series, and gets curb stomped every time he's encountered, and the fact that [[LegacyCharacter there were multiple Metal Sonics rather than one didn't help]]. Not only fans, but even ''Sega'' got tired of this and told series writer Ian Flynn to knock it off, and even he admits he's wanting it avert this with Metal in the future.
* BaseBreaker: Princess Sally. Oh, ''Princess Sally.''
** Many of the authors for the comic.
** [[spoiler:Geoffrey St. John.]]. Some people see him as a sympathetic guy who was fed a bunch of lies as a child which lead him to making the biggest mistake of his life which he regrets wholeheartedly. Other see him as a boy who was fed a lot of lies as a child but should have know better than to trust Naugus a known Villain and a jerkass who crosses several moral lines by betraying and/or manipulating his friends who are citizens in the country his is trying to protect. Added points for the latter seeing how he knew his wife would be against any of this from the start.
* BrokenBase: SeasonalRot is largely the cause of this. Where did the DorkAge start? Where did it end? ''Did'' it end? Was Sally's {{Chickification}} justified, or was it a hideously huge breach of established character just to [[ShipSinking sink the fanbase's largest ship]]? The typical benchmarks are that the series started to decline after ''Endgame'', took a full-on nosedive during the Bem/Xorda arc, and has only started recovering since issue #160 with Ian Flynn being head writer.
** Arguably applies on a much wider scale. [[BrokenBase There's the Sonic fans who love the comics and those that despise it.]]
** The reboot's set of a whole new schism among fans between those who like it and those who don't.
* CanonSue: Though he was accepted by most of the fanbase, Knuckles started turning into this after a while. Being part of a vast lineage wasn't the end of it, he eventually came to have an important prophecy associated with him and took on powers that allowed him to warp reality as he saw fit. At its peak, Knuckles started to eclipse Sonic in importance, and one storyline set in the future revealed that Knuckles ''destroyed Robotnik'', who was Sonic's main villain and rival. Add onto his his previous friendship and relationship with Sally, and you get the distinct impression that Knuckles had pretty much taken over the comic. Recently, however, they've started to balance this, with Sonic taking the reins back as main character, and him, Tails, and Knuckles being defined as Mobius's quintessential PowerTrio.
* CompleteMonster: [[Monster/SonicTheHedgehogComics See here]]
* ContinuityLockOut: The first couple of issues of ''Sonic Universe'' have this problem. #1 gave such a quick summary of ''Sonic Rush Adventure'' that only people who played the game knew what was going on. Also, #1 continued from ''Sonic X'' #40 (a whole different series), which continued from ''Sonic the Hedgehog'' #196, which was part of a large story arc from the main series. #2 was an adaptation of ''Sonic Adventure 2'' (probably an attempt to explain how it ''did'' fit into the continuity, as the original adaptation didn't really tell the reader much of anything about the game's story or how it fit into continuity), but would probably be pretty confusing to anyone who didn't play the original game.
** This may be why the Sonic the Hedgehog comic offering for the 2009 Free Comic Book Day was more of a lengthy synopsis about the characters and the story than anything else...
** It should be noted that they can't get too into the ''VideoGame/{{Sonic Rush|Series}}'' side of things, as they're apparently forbidden from using Eggman Nega beyond a few ominous references. ...And one "Off Panel" strip.
* CrazyAwesome: ''Omega''. The [[BloodKnight enthusiasm with which he enjoys destruction]] mixes perfectly with his [[{{Hammerspace}} impossible ordinance load]].
-->''But I still have five more salvos!''
-->''Yippie-ki-yay, pastel-colored resistance!''
-->''What? She left trees standing.''
** There's also Bean The Duck, an insane CloudCuckoolander duck who throws bombs at everything and loves shiny things, and Captain Metal, a crazed version of Metal Sonic who has become a stereotypical pirate that makes hilariously bad jokes and puns (such as saying that Blaze and her allies that their acting crabby right before revealing that he's given himself a ridiculous crab body) and plans to take over the world using the dimensionally displaced Wily Egg (renamed [[IncrediblyLamePun the Egg'O'War]]).
** Dr. Robotnik seems to be developing into this under Ian Flynn's pen, similar to his game counterpart.
* CreatorsPet: A character was introduced named Tommy Turtle, a childhood friend of Sonic that had never been mentioned before, but had once taught him a valuable life lesson. He died in his first appearance while performing a HeroicSacrifice to save Sonic, but about a year later was revealed to not have actually been killed and was brought back. Unfortunately, after bringing him back, the writers didn't seem to have any real idea what to do with him, and attempts to make him more relevant (such as having him become infested with nanobots, causing him to develop ''{{Transformers}}''-esque abilities) ended up just appearing ridiculous and making fans hate him. In Sonic Grams while Archie staff admitted that they knew a lot of their fans hadn't liked the character, they'd hoped they could change their tune, showing the clear divide between the staff at Archie at the time and the people actually reading the book. In the end writer Ian Flynn said when compiling a list of the comic's most unpopular characters, Tommy still ranked very high among the fanbase despite efforts to make him popular by previous writers. Tommy was therefore killed off (performing ''another'' HeroicSacrifice) and hasn't been seen since.
** Different writers have met criticism over over usage of certain cast members. Ken Penders was noted for his expansion of the Echidna brotherhood, which by the end of his run had its population and story background bloated to a convoluted rate. This treatment did not seem mutual with later writers, who decided to limit their numbers and had numerous Echidna characters KilledOffForReal. Ian Flynn however has been noted for his recent usage of Sally Acorn, reestablishing her as an active Freedom Fighter and love interest for Sonic and giving her a fairly notable role in nearly every arc (ranging from main character to prominent supporting character). Granted in both cases there are still [[BaseBreaker a fair amount of supporters]], though it's obvious the fanbase is very polarized by their heavy usage in the comics.
*** To be fair of Sally, up until Ian took over, Sally had been through a major Chickification during the comic's DorkAge, so trying to reestablish her as an ActionGirl once more through heavy usage to reestablish what she can do is probably sensible. However Sally, under Ian's and everyone else's pen, gets rather consistent flak for over usage at the expense of other characters and being a rather clear cut case of PositiveDiscrimination, garnering complaints for being blandly lucid and hyper competent (or at least most attempts at making her flawed being much more superficial than the other characters), her prime role also being to act as TheStraightMan as Sonic and punctuate his negative qualities. The fact Ian released a blog consisting of nothing but how awesome a character Sally is doesn't help much.
*** As for Knuckles and the overexpansion of the Echidna brotherhood, a lot of it was due to the fact that Ken Penders just would not look between the lines over what could be done with Knuckles, instead seeing him in a ''carte blanc'' state so he could make his own world instead of building off of Sonic. His devotion to the characters has gotten to the point where [[SmallNameBigEgo Penders has proclaimed that he was the reason Knuckles became so popular]], going so far as to proclaim that Sega was trying to focus more on ''Sally'' than Knuckles[[note]]While it ''is'' true Sega was trying to bolster up Sally in some way around '96, whatever plans they had never surfaced and that Knuckles had major pushes over the years without Penders' help.[[/note]]. It's also telling that the man refuses to use other people's characters other than his own and outright refuses to acknowledge what others have done to his character.
* DracoInLeatherPants: You'd be surprised just how many pictures there are on Website/DeviantArt of this comic's villains in suggestive situations, but it's perhaps [[http://cacti.deviantart.com/art/Deceptive-Interception-93010581 this one takes the cake]].
* EnsembleDarkhorse: Among the comic-only characters, Scourge has a large following (his girlfriend Fiona Fox and the rest of the Suppression Squas are a semi-case too through association), as do Mina Mongoose and Dr. Finitevus. The fandom rejoiced when [[AdventuresOfSonicTheHedgehog Scratch, Grounder and Coconuts]] were revealed to be returning after more than 100 issues of absence.
** Nicole, Sally's handheld A.I., had been an ancillary character since almost the beginning of the comic. Then along came Tania Del Rio's "Stargazing", which gave her a Mobian form and sent her popularity right through the roof -- and Nicole subsequently catapulted to Major Character status, overtaking even longstanding characters in the fanart department since her debut and never halting since.
** Shard the Metal has become pretty popular as well.
** Metal Sonic is a ''massive'' Ensemble Darkhorse in the rest of the franchise, but his portrayal here as a RedshirtArmy of drones with no personality was widely seen as VillainDecay. The new Metal Sonic introduced in issue 50 of Sonic Universe was thus massively popular for a) actually having a personality, b) bringing Metal closer to his canon portrayal, and c) being a OneManArmy that made the character scary and badass again.
* EpilepticTrees: There are many fans who believe that Lien-Da and Finitevus were involved at some point during the ''X Years Later'' timeline, and that he's the father of her son Rutan (this being mostly due to the fact that the tips of Rutan's dreadlocks are white, like [[EvilAlbino Finitevus' fur]].)
* EvilIsCool: Pretty much any villain that isn't a ButtMonkey. Notable stand-outs are Dr. Robotnik, Scourge, Mammoth Mogul, the Dark Legion, and Dr. Finitevus.
* EvilIsSexy: Lien-Da. A sexy as hell Echidna girl in skintight leather and a habit of whip wielding? What's not to like here?
** The Iron Queen has more than a few fans too. As does Finitevus, Scourge, Fiona, and (disturbingly) Snively and Eggman.
** Nicole's lynx avatar doesn't look half bad. [[BrainwashedAndCrazy Iron Nicole]] looks even better.
* FandomRivalry: With Fleetway's ''SonicTheComic''.
* FurryFandom: Go to Website/DeviantArt, type in echidnas, and see how many people represent themselves as echidnas. We'll wait.
** Hedgehogs - particularly [[ShadowTheHedgehog ones with pinstripes]] - and two-tailed foxes are equally common. Most blame the comics and the [[WesternAnimation/SonicSatAM SatAM cartoon]] for this most directly.
* FranchiseOriginalSin: A lot of the problems with Ken Penders and Karl Bollers's run (too many plot points, too much focus on people other than Sonic, inconsistent art, etc.) later down the line can be traced back to their critically acclaimed earlier days (storylines like "Endgame" and "Metal Madness" are considered excellent to this day). The difference is that back then, the two weren't engaged in constant [[CreativeDifferences petty fights with each other over the comic's story direction]] and the Echidnas weren't [[CreatorsPet Ken's pets]]. That coupled with the lack of a solid threat or plot now that Robotnik was dealt with, caused the comic to slip into it's infamous DorkAge.
* GrowingTheBeard: It's generally agreed that the comic became genuinely good around the issue 25 mark (which introduced [[EnsembleDarkhorse Metal Sonic]] into the comic and was where the comic developed an actual plot). It lost it's beard during the comic's DorkAge and there's debate as to where or if it regrew; some feel that Ian Flynn taking over restored the comic's respectability, others see the reboot as the comic finally doing away with the massive ContinuitySnarl and unmanageably large cast (not to mention Sega personally intervening to end Metal Sonic's BadassDecay and get rid of the RomanticPlotTumor), and of course there are those who feel that it ''never'' regrew.
* HilariousInHindsight: The images of Knuckles turning into Super Knuckles in issue 141 are similar to the final boss transformation montage in ''[[VideoGame/MegaManZero Mega Man Zero 2]]''. While they haven't gotten to that point, ArchieComics now publishes ''[[ComicBook/MegaMan Mega Man]]'' [[ComicBook/MegaMan comics]].
** In ''VideoGame/SonicColors'', Sonic lets out a BadassBoast that no copyright law in the universe could stop him. As you can see, so far, the comic's still going.
** In issue 161, Scourge has a shot much like the one that years later [[Series/{{Sherlock}} Moriarty would use]] in the promotional pictures. Inspiration from one ManipulativeBastard to another, perhaps?
* HarsherInHindsight: From his first introduction Silver mistakenly thought the Freedom Fighter Traitor was Sonic to counter his first sega in game appearance. His Second guess was really made in Sonic Universe 6 where upon realizing the Freedom Fighters disbanded because Queen Sally thought they were no longer needed. Silver guess this but for the first and only time he thought he was wrong. Fast forward a couple hundred comics later and it turns out he was somewhat right.
** Issue 3 had everyone think Robotnik got hold of atomic bombs and went over the destruction the weapons could cause. While it turned out he had only gotten a bomb to be used against bugs, later on Robotnik ''did'' get atomic bombs. Robo-Robotnik wiped out Future Mobius with them, and Robotropolis got nuked by missiles.
* HolyShitQuotient: High during the [[WhamEpisode wham episodes]] and milestone issues, but the "Endgame" and "Countdown to Chaos" story arcs stand out in terms of sheer HOLY SHIT inducing moments.
* IdiotPlot: Done at times, most frequently (but more intentionally) in the earlier comical issues. The Iron Dominion arc in particular dangles a long time for the same of climax build up, relying too much on the entire Freedom Fighter squad being blindly overconfident enough to give the villains blatant advantages (eg. letting Snively go free and ignoring his activity after Eggman's defeat (despite his usual track record), oblivious to the harm a super powered techno mage may have on a city ''completely composed of artificial life''). Sally at least has the decency to Lampshade these were exceptionally stupid moves afterwards, but all the same, surely someone else had enough brain cells to see it coming.
** An example is the ''Endgame'' arc. Dulcy explains that dragons are [[LivingLieDetector able to sense truth]], something treated as common enough that Geoffrey St. John, Knuckles, and Espio believe that Sonic's been framed for killing Sally. ''No one'' questioned why she wasn't called in before, especially since this story was about the ''third time'' Sonic's been framed for treason. Also, it was revealed earlier in Sally's mini-series that Robotnik could make robots that flawlessly imitate real people, so there was no real reason for everyone to take this at face value.
* InternetBacklash: As mentioned below, the entire Ken Penders debacle.
* ItWasHisSled/ LateArrivalSpoiler: At this point, if you don't know that [[spoiler:Sally was roboticized in issue 230]] then you have been living under a rock. Not that it matters, since in the RetCon she isn't roboticized anymore.
* JerkassWoobie: [[ManipulativeBitch Strange]] [[ChronicBackstabbingDisorder as]] [[ConsummateLiar it]] [[HarmfulToMinors sounds]], you could actually make the case for [[DarkActionGirl Fiona]]. She really does have serious abandonment issues and her self-esteem is such that she'd sooner stick by a womanizing creep like Scourge over Sonic when the latter started to question her loyalty to him. Even WordOfGod has hinted that she's still not ''all'' bad.
** Scourge himself gets this treatment toward the end of the "King Scourge" arc, even to the point of shedding tears.
** Snively is also a classic example. Nothing goes right for the poor guy in his life, so you pity him...but he brings so much of these problems upon himself due to his treacherous nature, so you also think he's an asshole.
* MagnificentBastard: Mammoth Mogul most certainly didn't fit the bill for this early on, even though he was clearly meant to be one. An immortal cavemammoth from earth's second Ice Age (it's complicated), Mogul was always plotting and scheming, with the writers trying their darndest to build him up with unlikely {{Evil Plan}}s for the stories. Nothing worked, and his world domination plans failed again and again and again. He spent more time being imprisoned than anything else. Then one day Mogul wised up and essentially said to the heroes "I just remembered that I'm immortal. So here's my new {{plan}}: I'll live in this sweet casino I just had built, amuse myself by taking pot shots at you whenever I can, and wait for you all to die of old age. I can beat you by outliving you."
** Dr. Robotnik has taken a ''major'' [[TookALevelInBadass step up]] into this after reasoning himself out of insanity. Probably the most notable example of this is "Genesis" where he successfully manages to manipulate everything so that he can ''rewrite reality itself''. And than after Sonic reverses his rewrite what does he do? Rather than take a total loss he roboticizes the injured Sally while Sonic is distracted, thus giving himself a deadly new weapon that Sonic is terrified of injuring. And he does all of this while ''casually drinking a glass of wine''.
* {{Misblamed}}: ''Ken Penders.'' [[LoveItorHateIt While the quality of his writing and art is an entirely subjective matter, ]] factions of the fandom would have you believe Ken Penders was the freaking Anti-Christ.
** He's often been blamed for the dissolution of Sonic and Sally's relationship in issue 134 – Karl Bollers wrote that issue. Ken himself was surprised and would've gotten them back together in later issues.
*** The recent lawsuit with Archie has resulted in many fans either getting their facts wrong or oversimplifying a complex legal mess. Here's the facts: Under the agreement that SEGA entered into with Archie, SEGA is meant to be the sole owner of all content in the books (writing, art, characters, and concepts). Archie is simply allowed to make and publish something SEGA owns. Archie, for its part, is meant to have all staff sign contracts agreeing to these terms. However Archie either failed to get some contracts, or lost them. When Penders realized this oversight, he filed for ownership of his work at the US copyright office, then posted a letter stating that Archie's use of his characters was unauthorized and illegal, that he was notifying distributors of that fact, and that he was considering legal action against SEGA/Bioware/EA for making Sonic Chronicles. Archie then sued Penders. Penders sued SEGA/Bioware/EA, but was told by the judge that he had to finish the case with Archie first. Archie couldn't produce a contract proving he had signed away ownership, but Archie still had their deal with SEGA (who Penders was suing), and SEGA was adamant that under the terms of the agreement they should own everything that had been in the comics. In the end Archie and Penders came to an unusual settlement. The full terms are unknown, but a major point was that Archie refused to contradict SEGA's claims of ownership, so Archie wouldn't agree Penders owned anything... they just wouldn't sue him for making anything containing the characters he'd created. The idea that Archie could simply license the characters from Ken ignores that Archie would have to agree Ken owns the characters to do that, and SEGA would never permit Archie to do that. (Keep in mind this summary is STILL a massive oversimplification...)
*** It should be noted that Penders was not simply seeking ownership of the characters to make new comics, he was seeking royalties for reprints of stories he wrote/drew, as per copyright laws, and because he felt said work was plagiarized into ''Sonic Chronicles''. According the the US copyright office, he owns the copyrights to the majority of the characters he created (Knuckles, excluded, obviously), and can use them in his upcoming graphic novel series, The Lara-Su Chronicles so long as the characters and setting do not resemble anything Sonic related. (The reaction to this revelation and the promo art has faced InternetBacklash for a laundry list of reasons, but let's not get into that.)
*** His workaround to explain how The Lara-Su Chronicles aren't too similar to Sonic? Lara-Su and her people aren't echidnas, or even animals at all. They're aliens, and their species name is “Echyd’nya”.
*** Penders has stated that Archie has the okay to use any of his characters as they see fit, so long as they a) pay him a fee like they do with Sega, b) consult him about plans concerning Julie-Su, Lara-Su, and Locke, and c) his ''Mobius: 25 Years Later" storyline is made the canon future.
**** Whatever Penders' intentions may be, his demands for the comic could not possibly be met due to the agreement between SEGA and Archie (SEGA only agreed to let Archie make a comic if SEGA ended up owning everything Archie made, right down to the characters. Archie's failure to manage paperwork correctly doesn't change SEGA's belief that they should own everything, and Archie's in no position to disagree. They simply can't agree to Penders' terms, since that would mean contradicting SEGA's stance that they own everything). Some of the fan-hate directed at Penders stems from his claims that Archie could use his characters if they agreed to his terms, since would be aware of how impossible those terms are from his time as head writer.
* {{Moe}}: Characters such as Cream, Aerial, and Athena
** Hope Kintobor to a lesser extent.
* MoralEventHorizon: The original Dr. Robotnik famously crossed it in "Endgame", as did Drago.
** Thrash has definitely crossed this when he [[spoiler: literally made Knuckles the last of the echidnas.]]
** Metal Sonic finally crosses it for good when [[spoiler: he seemingly murders Shard.]]
*** [[spoiler: Eggman and Metal Sonic cross it yet again in the ''Mega Man'' crossover by trying to ''murder Dr. Light''. Even Dr. Wily is disgusted by them after that.]]
* MyRealDaddy: Ian Flynn is considered this for Scourge for giving him a cool and distinctive new look and making him into a more intimidating and complex villain instead of the stereotypical EvilTwin he was before.
** Some fans go further with this and consider Flynn the real daddy for the comic in general, though this view is ''very'' [[BrokenBase far from universal]].
* NeverLiveItDown: Many fans aren't willing to let Sally live down the time she slapped Sonic in anger.
* RescuedFromTheScrappyHeap: Silver of the much maligned ''Sonic the Hedgehog 2006''. His comic version is liked a lot more because his personality has been changed to a guy who is not very confident in his abilities as a "SetRightWhatOnceWentWrong" guy. Silver was like that though, but his comic counterpart is much less annoying about it, and is (slightly) more easy to reason with.
** Antoine through CharacterDevelopment for many who considered him TheScrappy in SAT:AM.
** Fiona Fox wasn't popular as a love interest for Sonic. Once she pulled a FaceHeelTurn, [[EvilIsSexy sexy]] EvilCostumeSwitch, and hooked up with [[EnsembleDarkhorse Scourge]], though, she became much more liked.
** Shadow and Rouge. For the longest time, the comic had no idea what to do with either of them after the ''VideoGame/SonicAdventure2'' adaptation (which was only ''one issue long''). As ''VideoGame/SonicHeroes'' was rendered moot due to comic events, using them for that was out of the question and the two would make sporadic appearances afterwards, Shadow working with Eggman and Rouge with Evil Sonic. It wouldn't be until Ian Flynn took over that both performed a HeelFaceTurn and lead into the creation of the much beloved Team Dark.
* RomanticPlotTumor: Plagued the comic for quite a long time. Luckily the comic has since moved on.
* RootingForTheEmpire: It's easy to root for the Dark Egg Legion. They do take orders from Eggman, but they aren't completely evil, and most of their members seem to be regular Mobians, bar the cybernetics. Given that the heroes are headed by Sonic, who can be a bit of a {{jerkass}}, and the Kingdom of Acorn, an incredibly ineffectual monarchy that can barely function, it's no wonder. And they're the only group in the ''world'' who don't actively despise technology. A great example is the Great Desert DEL. They were turned into mindless Robian mooks thanks to UnwillingRoboticisation and forced to fight the Sand Blasters, an extremist group of Freedom Fighters. After being turned back into Mobians, they tried to make peace with the Sand Blasters, but where instead hit with FantasticRacism for being former Robians. In order to survive, they went to Eggman for help, who legionized them. When The Baron, leader of the Great Desert DEL, was confronted about this by his niece, hero Bunnie Rabbot D'Coolette, he responded that being in the DEL isn't so bad. Being legionized means cybernetic upgrades, which in turn make for an awesome health plan, as The Baron pointed out, when he thanked legionization for fixing his "bum knee". He also mentioned something about D'Coolette's being oppressors, which insinuates FantasticRacism within the Kingdom, making them look even worse.
* TheScrappy: Tommy Turtle probably got it the worst, but Dulcy and pre-Character Development Antoine had no few detractors. Mind you none of them had ''anything'' on [[SonicX Chris Thorndyke]].
** Post-Character Development Antoine gets it bad too. The fanbase seems divided whether he was originally an annoying one-note Jerkass, or if maturing his character robbed him of his defining characteristics and made him bland. The poor guy just can't win.
** There's also [[{{Jerkass}} Drago Wolf]], a traitor to the Freedom Fighters who was also [[DomesticAbuse an abusive dick to his girlfriend]] and soared over the MoralEventHorizon in "Endgame". He's a massive douchebag and later on joined the comic's resident PsychoRangers which he promptly contributed absolutely nothing too (in fact he was TheMillstone to them). ''No one'' likes him in-universe or out and Ian Flynn has gleefully admitted that he only brings the guy around when he wants someone to be beaten up.
* SoBadItsGood: The early comics were pretty much this, being funny due to how lame the jokes were at best. Once it started developing an actual plot, the comic became just straight up good.
* [[SignatureScene Signature Story Arc]]: The "Endgame" story arc, which is probably the only storyline in the comic that is universally considered great. It's also famous for cementing the transition to plot-driven stories and killing off the original Robotnik.
* StrangledByTheRedString: Antoine and Bunnie Rabbot were thrown together in Endgame with almost no build-up beyond the same issue they got together revealing that Antoine had once saved Bunnie's life. Thankfully, the relationship was well handled ''after'' that point, and it was easier to accept than most examples because neither of them had any romantic chemistry with other characters.
** To their credit, though, Antoine and Bunnie ''did'' show a subtle interest on each other when they first saw the other way back in issue #3 (with a few panels of difference, mind you, but the fact remains). There was also the backup story in issue #23 which included Bunnie saving Antoine's life on a mission, and Antoine kissing her in gratitude. When reprinted in Sonic Archives Volume 4, the creators acknowledge that story as the beginning of their impending romance.
** Worse off is the Echidna race - according to WordOfGod, echidnas have what is called "the Soultouch" - a SixthSense that also acts as a literal Red String for them and that once they've found their soul mate, they pretty much stay together, although there are some exceptions. This is why Knuckles and Julie-Su hooked up only after 24 issues and why he hasn't been never up with her.
* StrawmanHasAPoint: Thrash admits he doesn't know exactly ''why'' the echidnas experimented on his people [[note]]it was to fight Mammoth Mogul's Order Of Ixis, viewed as a horrible crime by echidna society, and would've been reversed had one of the Knights of Albion not turned into the second Enerjak and crippled the civilization at the time[[/note]], thus making his "justice" more like revenge. But between the Brotherhood of Guardians never fighting Robotnik at all, Albion not getting involved either, the Dark Legion, Enerjak incarnations, and a chapter of the Dark Legion willfully joining Eggman for power (they were trying to recruit the rest of their species into Eggman's army when last seen), he's not exactly wrong in his views.
** Mina is depicted as being overzealous and callous for making a public statement about how dangerous NICOLE is and indirectly starting a mass paranoia concerning her. However, as sympathetic as she is, NICOLE was shown to be extremely dangerous as a result of the Iron Queen corrupting her programming, leading to a takeover that led to the Mobians being enslaved and many supposedly legionized (IE. mutilated with cyborg implants). The Freedom Fighters are outraged by Mina's actions and labelled the public as being vindictive, but as she angrily pointed out, people had suffered because of NICOLE, and largely because they were cocky enough to make a huge oversight (it was implied they were taking precautions by that point, though had neglected to console the public about it, and even then it was too little too late for some).
** Similarly Hamlin is conveyed as smug weasel who uses a long lived grudge against Sally to try and get the council to persecute her for disobeying orders. However, Sally was the one who created the Council in the first place, and then nonchalantly ignored them when they attempted to make a democratic tactic. When Hamlin pointed out she was undermining their entire purpose (with some other members even agreeing there was substance in this), she gave up her refute and outright blackmailed the Council that she would refuse to help at all. The fact that she so quickly assumed Hamlin only accused out of spite (he had, but he had yet to admit it, and his argument had some ground regardless) and moaned how he could have the heart to call her out only further emphasized her self righteousness on the matter.
*** While we're supposed to side with Hamlin over his team's being mistreated and forgotten by the Freedom Fighters, despite ''being'' an actual team that Sally personally trained, it falls apart because that team was called the ''Substitute'' Freedom Fighters. By definition, they go into action when the regular line up can't. Also, his team was led by Larry Lynx, who ''did'' volunteer to help Rotor in the past so Hamlin and his teammates could've just asked to help out.
* StrawUtopia: It isn't hard to see Mobotropolis (under Ken's penmanship) and Echidnaopolis and Albion as beautiful utopias that only had a few blights to them. Mobotropolis is even more telling as the back stories for the setting tend to paint the kingdom as a peaceful place in stark contrast to the Overlander's Megaopolis, which is shown to be incredibly destructive and polluting. However, under Karl Bollers' penmanship, Echidnaopolis and Albion was ravaged to the ground and, under Ian's penmanship, the rulers of Mobotropolis were seen as idiots who were lead by a mystical force that led them to make incredibly bad decisions. In fact, even after the monarchy turned into a republic, it was shown that most (four out of seven) of the councilors had some grudges with the royalty. To say nothing that those same four councilors just aren't the kind of people you'd want to have a position of government, having very little leadership experience and possibly questionable mental health.
** A rather Fridge horrific example as Mobotropolis, Echidnaopolis, and Albion seem almost afraid of change. Mobotropolis and it's people rarely developed anything new outside of what the Freedom Fighters use and even the citizens want to bring the old Mobotropolis back and never want to develop anything more or integrate more people into it. Echidnaopolis is worse as it never helps anyone but Echidnas grow but it bans the use of technology as they see it as evil, ignoring the fact that they not only still use it, but could still advance if they were more careful with ''how'' they used technology[[note]]For instance, don't make a device designed to siphon huge amounts of Chaos Energy something that the user wears on their body.[[/note]]. Albion is the worst as it's an echidna only society and believes all echidnas should live their cut out from the rest of the world. They even go so far as to not correct the mistakes they made in the past.
* SuetifulAllAlong: Many are accusing Sally of leaning into this. Attempts have been made to place Sally in a flawed light due to her emotional outbursts, with later strips lampshading her treatment towards Sonic. However, it is only Sally herself that comes to this conclusion, which generally only leads others to sympathize with her {{Heroic BSOD}}s and [[CreatorsPet comfort and justify her actions]]. The fact that the current writer released a blog on how wonderful Sally is (notably consisting solely of less than discript positive traits) doesn't help this at all.
* TakeThatScrappy: The only reason Drago Wolf's kept around is to be the ButtMonkey of the cast, in stark contrast to the [[AlasPoorScrappy reaction]] [[spoiler: Tommy Turtle]] got.
* TheyJustDidntCare: While the writing may be [[BrokenBase subject to debate]], some of the artwork shows that whoever was in charge couldn't really give a dang, with issue 113 and the main story of ''Sonic Super Special'' issue 15 being so poorly done artwise that one has to wonder how they even got published in the first place. And then there was a issue in the ''Sonic Quest'' miniseries in which they forgot to remove one of the notes left by the artist to the colorist, so there's a hand-written line outside of a panel that reads "REMOVE RED LINE'S" in one of the pages found in the printed version of the comic. [[http://imageshack.us/photo/my-images/542/ohshit.png/ It must be seen to be believed.]]
* TheyWastedAPerfectlyGoodCharacter: A major problem with the comic, especially during the Penders/Bollers era. Because of how these two men operate, established Sega-based characters and characters created by other writers tend to get knocked to the wayside or not even introduced. For instance, EnsembleDarkhorse Bean the Dynamite Duck and Bark the Polar Bear were first introduced game-wise in ''VideoGame/SonicTheFighters'' in 1996. It would be 10 years later, in issue #160, that they'd appear in the comics. There's also the Bird Armada for '''VideoGame/TailsAdventure'', which didn't show up into the comics for ''15 years''. Comic wise, for example, the Iron Queen. She first appeared in issue #60. She is not heard from again for 140 issues.
* TheyWastedAPerfectlyGoodPlot: Issue 172 probably holds one of the most blatant examples, in fact, a double. First, after Fiona tells Tails that he can't count on anybody before slapping him across the face, she sets Sonic as her prime example due to him leaving her imprisoned back in the mining camp (in the 28th issue of the Knuckles The Echidna comic). Sonic attempts to overrule her point by starting off with "That's no excuse to..." before ending up in another physical spat with Scourge, along with Fiona just tell him to "shut up already". Second, when Sonic and Scourge confront each other about why Fiona chose to be with Scourge, Scourge points out that the only way for Sonic to be like him would be "one bad day", which causes Sonic to counterattack by pointing out that Scourge would be just like him if he showed "a little bit of selflessness" and "a little bit of decency". Scourge is completely at a loss for words at this point... until Fiona abruptly intervenes and kicks Sonic aside, claiming that he "had [his] chance". She even goes on to put him down by claiming that he's a weakling by holding back and that "it's all about survival of the best".
** Issue #108 would also count, having both the original and the new Dr. Robotnik together in the same reality...only to have them dink around for a third of the issue before the old one disintegrated.
** This is a big complaint about Ian's post-"cleaning up" works, up to and including the Iron Dominion saga; many plot points he brought up during this time (such as the revolution of the Kingdom of Acorn into a republic and Eggman going insane) had lots of potential for interesting stories of their own, but were notoriously prone to SnapBack fever. In fact, this became one of the biggest reasons, alongside PacingProblems, for why even die-hard Ian fans like to hate on the Iron Dominion saga.
* UnfortunateImplications: In retrospect: One of the most controversial topics of the comic is Rotor's WordOfGay reveal. Ken Penders had indicated on his message board that a major character in Mobius: 25 Years Later was gay. It was possible to deduce that said character was Rotor. However, before anything became official, Ian Flynn took over, and in his version of Mobius: 25 Years later Cobar was brutally killed and Rotor subject to ColdBloodedTorture. Then, the official reveal came out that the gay couple in question was, in fact, Rotor and Cobar. [[BuryYourGays Oops]].
** [[http://www.bumbleking.com/forum/viewtopic.php?f=4&t=5334 Years later,]] Flynn commented that he would have approached things differently had he known they were meant to be a couple.
** The reason Ken Penders wrote Rotor as gay was because he wanted to explain why Rotor was shy and [[AmbiguousDisorder not socially adept like the others]]. [[SarcasmMode Because only gay people are shy around others.]]
** From a certain point of view, the Felidae could qualify; they are a feline race of Mobians whom look far more bestial and animal-like than other Mobians, and have a civilization that has gone unchanged for millenia, all the while having mentioned practicing things such as cannibalism. The Felidae live in what is basically South America, and have an architectural and clothing design-philosophy that tends to bring forth stereotypes of ancient Meso-America and Africa. They are generally portrayed as being primitive and savage compared to other Mobian... so basically, they're a kind of anthropomorphic version of FrazettaMan. While they've been fleshed out a bit since they're debut, it's still a bit of a brow raiser.
** Penders seems to have issues with women in power. The Brotherhood of Guardians has only one female in it's history. Said female was poisoned unlike the surviving members, which include her ''great-grandfather'', who are still active. He originally planned to kill Sally off in Endgame because he felt that having her dad around made her redundant, and it was made clear that she couldn't take the throne without marrying someone first.
* ValuesDissonance: Covering everything from the systems of government on Mobius to the clothes the characters don't wear.
** The Felidae in particular have a lot of this, often tying into their BlueAndOrangeMorality; they have a culture and society that tends to be pretty harsh by the standards of others, but for the Felidae it's the most natural way of doing things. And that's without getting into their views of clothing... to put it mildly, the Felidae are VERY literal-minded when it comes to official costume and dress; from their viewpoint, what you wear literally determines WHO you are. It's rather confusing to outsiders.
* VillainDecay: Mammoth Mogul, Ixis Naugus, Dr. Robotnik, and Metal Sonic all suffered this at various points in the comic (Mogul's plans always failing, Robotnik becoming a bumbling fool, Ixis becoming crazy, etc.). Fortunately this is almost always dealt with in some way or another such as having them suddenly making a big comeback or being reasoned out of the insanity that caused their decay.
* WordOfGay: The original writer of ''Mobius: 25 Years Later'' has confirmed that Rotor and Cobar, an Echidna scientist, were both gay and in a relationship together.
** [[ShrugOfGod Shrug of Gay]]: Neither the current writer, Archie or Sega have confirmed or denied this as canon though, and there are no conclusive hints, so it may not be all that relevant.

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