Accidental Aesop: 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. Similarly many arcs involve the heroes making Fire-Forged Friends with previous adversaries or being forced to let go of previous grudges, a lot of which were formed by hubris and poor communication (eg. Sonic with Knuckles, Monkey Khan and Silver).
Accidental Innuendo: Almost certainly unintentional, but still: Lupe comes from the word Lupa, which is Latin and means either she-wolf, or, well...
It's generally agreed that "Iron Dominion" overstayed its welcome. Some are willing to forgive for setting up the epic "Genesis" story arc, but this is far from universal.
Some also blame the unfinished Mecha Sally arc as much on it's lagging pace as the copyright enforced retcon. Had it been padded less excessively, the original continuity could have possibly gotten a more proper ending.
The "Shattered World" arc is starting to lean into this since it's been going on for a year now. The "World Unite" crossover popping up in the the middle of the story and delaying things is not helping matters.
Archive Panic: It can be hard to get into the comic at first because of its 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.
Author's Saving Throw: 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-Sonic the Hedgehog/Mega Man: Worlds Collide 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.
Many of the authors for the comic, especially Penders, Bollers and Flynn.
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.
"Sonic Live" (in which Sonic and pals travel to the real world and interact with real kids) and Super Special #17 (a crossover with characters from Image Comics of all places). So much so that neither is considered canon by fans or the creators.
Seasonal Rot is largely the cause of this. Where did the Dork Age 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 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.
The reboot's set off a whole new schism among fans between those who like it and those who don't.
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. It should be noted that they can't get too into the Sonic Rush side of things, as they're apparently forbidden from using Eggman Nega beyond a few ominous references. ...And one "Off Panel" strip.
This is the fate of the pre-Nu252 comics because it relies so much on characters and concepts created by people not named Ian Flynn.
There's also Bean The Duck, an insane Cloud Cuckoolander 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 the Egg'O'War).
Dr. Robotnik seems to be developing into this under Ian Flynn's pen, similar to his game counterpart.
Creator's Pet: 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 Heroic Sacrifice 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 anotherHeroic Sacrifice) 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 Killed Off for Real. 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 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 Dork Age, so trying to reestablish her as an Action Girl 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 Positive Discrimination, 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 The Straight Man 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 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 Knucklesnote 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.. 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.
Not the comic itself, but the Endgame story, once considered one of the best arcs of the comic, is getting less and less loved over time, thanks in no small part to Penders' actions. Many, if not most are considering it an Idiot Plot.
The Knuckles comics have also been getting this, for the same reasons. It used to be considered better than the main comic, but now many lump it in with Penders' other work.
Die for Our Ship: Relic the Pika got hit with this the moment she was introduced, both by Knuckles/Rouge shippers and fans of Julie-Su, who felt that introducing another potential love interest for Knuckles so soon after Julie-Su was purged from the comic was hitting a nerve. Notably, she and Knuckles aren't actually romantically involved, and despite some noticeable Ship Tease, Ian Flynn has said he has no plans to make them a couple.
Ensemble Darkhorse: Among the comic-only characters, Scourge has a large following (his girlfriend Fiona Fox and the rest of the Suppression Squad are a semi-case too through association), as do Mina Mongoose and Dr. Finitevus. The fandom rejoiced when Scratch, Grounder and Coconuts were revealed to be returning after more than 100 issues of absence.
One of the few major Brotherhood member to get any big artwork was Spectre, who has one of the most imposing appearances of anyone in the comic.
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.
From the new reality, Eclipse the Darkling has become rather popular as well. Also, when Breezie the Hedgehog made a triumphant return after near 20 years of absence, the fandom's reception has been overwhelmingly positive.
Metal Sonic is a massive Ensemble Darkhorse in the rest of the franchise, but his portrayal here as a Redshirt Army of drones with no personality was widely seen as Villain Decay. 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 One-Man Army that made the character scary and badass again.
Epileptic Trees: 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 Finitevus' fur.)
Evil Is Cool: Pretty much any villain that isn't a Butt Monkey. Notable stand-outs are Dr. Robotnik, Scourge, Mammoth Mogul, the Dark Legion, and Dr. Finitevus.
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. Iron Nicole looks even better.
Fan Discontinuity: There are a good number of people that refuse to read the comic after the reboot for two main reasons:
The first reason is for removing every character not owned by Flynn or created by SEGA from the comic.
The second reason is for how it was executed. The final storyline before the comics' reboot was not given a proper ending and so many questions and problems were left unanswered (We'd list them, but there are so many, it would likely result in a Wall of Text.) Things would have been fine if the final storyline had a proper ending instead of giving it a combination of No Ending and Cliffhanger, but because it didn't many people wish that they would have finished the old storyline instead of ending it the way it ended. For those reasons, many old readers of the comic refuse to read the new continuity.
Clashes also tend to erupt with dedicated fans of the games continuity, with many arguments over which incarnation of the franchise is better and more definitive.
Franchise Original Sin: 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 petty fights with each other over the comic's story direction and the Echidnas weren't 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 its infamous Dork Age.
It's generally agreed that the comic became genuinely good around the issue 25 mark (which introduced Metal Sonic into the comic and was where the comic developed an actual plot). It lost its beard during the comic's Dork Age 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 Continuity Snarl and unmanageably large cast (not to mention Sega personally intervening to end Metal Sonic's Badass Decay and get rid of the Romantic Plot Tumor), and of course there are those who feel that it never regrew.
This definitely seems to apply to the 4-issue "Champions" Arc. The reception has generally been positive as most readers note that its probably the best the comic has been in a while. Highlights include, a revamped Ensemble Darkhorse in Breezie, amazingly expressive and vibrant art, and a more character driven plot than what the series usually tries.
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.
Some fans have noticed that this panel from the old Knuckles comic is a pretty accurate depiction of Penders and what he caused with the lawsuit.
Its either this and/or Harsher in Hindsight, but in October 2013 we saw the release of The Complete Sonic Comic Encyclopedia, which pretty much tells us everything that has happened in the comics since it's release and information on the characters. Unfortunately, this was released five months before the comic's reboot due to the Ken Penders lawsuit. So the encyclopedia covers almost everything that happened in the Pre-Super Genesis Wave timeline.
In issue 19, Sonic teams up with several of his alternate counterparts from other worlds to stop Robo-Robotnik; one of the counterparts is a Batman version. Nearly 20 years later, Sonic's current voice actor becomes Batman.
Holy Shit Quotient: High during the wham episodes and milestone issues, but the "Endgame" and "Countdown to Chaos" story arcs stand out in terms of sheer HOLY SHIT inducing moments.
Idiot Plot: 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 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.
Iron Woobie: Sonic himself. He never lets any of the crap that he gets put through keep him down for long. Even the absolutely brutal Darkest Hour in issue 175 doesn't stop him and he manages to flip it back onto Robotnik 25 issues later.
It Was His Sled: At this point, if you don't know that 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.
Jerkass Woobie: Strangeasitsounds, you could actually make the case for 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 Word of God 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.
Dr. Robotnik during the "Darkest Storm" arc where he's tricked into murdering his own surrogate daughter Mecha Robotnik, the only person he ever truly cared about. At the end of the story he actually lets Sonic walk away sadly commenting that "I've lost a lot today".
Even if your not a fan of him, Geoffrey St. John is definitely one. He felt that working with Naugus would help the Acorn Kingdom in the long run. Remember, when he first met him, he had no idea that Naugus was evil because he was a kid when he first met him and his father had just died so he wasn't emotionally stable. When he does learn that Naugus was Evil All Along and that he wanted to control the council, he hated that idea and he wanted to back out, but Naugus reminded him that there was no way he could stop him. When Silver sits to talk with him later on about how working with Naugus is bad, Geoffrey agrees with him but he says that it's too late for him to change. Geoffrey had good intentions and he believed working with Naugus would have good outcomes. It's too bad things didn't work in his favor. Even worse, because of the comics' reboot in 2013, which removed all characters not written by Ian Flynn or SEGA characters, he will never get a chance to redeem himself.
Les Yay: Arguably, between Sally and Nicole in the Spark of Life storyline. Sally seems to be closer to Nicole than to anybody else, and gets extremely pissed off at Nicole's creator for considering her a failure. Nicole, meanwhile, constantly makes glasses at Sally, teases her, and specifically wanted to see the stars the way Sally did in a flashback.
Magnificent Bastard: 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 Plans 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 majorstep 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.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. A lot of the anger and hatred towards Ken Penders stems from the infamous lawsuit that forced the Continuity Reboot on the title. Though the reasonings and the outcome for all of this have not yet been revealed and may never will, many fans blame Penders due to the fact that they feel that his actions were motivated by greed and jealousy, which isn't helped by his constant declarations that he's trying to get fair payment for reprints of past comics for all workers and, upon the settlement, declaring that he was going to get to work on The Lara-Su Chronicles.
ADAM tricking Robotnik into killing Mecha Robotnik. Even with how evil Eggman is that was just pointlessly cruel.
Thrash has definitely crossed this when he literally made Knuckles the last of the echidnas.
Metal Sonic finally crosses it for good when he seemingly murders Shard.
My Real Daddy: 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 Evil Twin he was before.
Some fans go further with this and consider Flynn the real daddy for the comic in general, though this view is veryfar from universal.
Never Live It Down: Many fans aren't willing to let Sally live down the time she slapped Sonic in anger. Even after repeated displays of remorse from the character, and even a Cosmic Retcon rendering it Canon Discontinuity, there are still fans who will hold it against her.
Out of universe, Ken Penders will forever be known as the guy who took away various characters and made a Continuity Reboot necessary.
Rescued from the Scrappy Heap: 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 "Set Right What Once Went Wrong" guy. Silver was like that though, but his comic counterpart is much less annoying about it, and is (slightly) more easy to reason with.
Shadow and Rouge. For the longest time, the comic had no idea what to do with either of them after the Sonic Adventure 2 adaptation (which was only one issue long). As Sonic Heroes 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 Heel–Face Turn and lead into the creation of the much beloved Team Dark.
Flynn has also with repeated vigour tried to rescue Princess Sally, mostly concerning her past Sue accusations and trying to present her as a more flawed character. While it's not a universal case by a long shot (some still debate whether he's made her worse), most fans at the very least have let go of her infamous outburst in the Home arc following some displays of remorse from her.
Notably, a number of her former detractors have reacted much more positively to the post-reboot version of Sally, for having a new design more in line with Sega's characters, being much more of an Action Girl (she was arguably a Faux Action Girl until then), and Archie quietly dropping her relationship with Sonic, allowing her (and Sonic) to develop as characters on their own. The Spark of Life miniseries was particularly good to her image, as it was the first time in a while that a story centered around her without relegating her to the role of a bit player (something even her own miniseries couldn't do).
Romantic Plot Tumor: Plagued the comic for quite a long time. Luckily the comic has since moved on.
Rooting for the Empire: 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 Unwilling Roboticisation 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 Fantastic Racism 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 Fantastic Racism within the Kingdom, making them look even worse.
The DEL's post-reboot counterpart, the Egg Army, also falls into this. While many Egg Bosses, such as Thunderbolt, are pure evil, others, like Clove and Nepthys, are treated sympathetically. Both only joined the Eggman Empire out of desperation rather than loyalty to Eggman (Clove joined so that Eggman could save her sister from a debilitating disease, while Nepthys joined to keep the Eggman Empire from completely taking control of Shamar by locking her division of the Egg Army into a stalemate with her longtime friends, the Shamar Freedom Fighters).
The Scrappy: 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 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 Drago Wolf, a traitor to the Freedom Fighters who was also an abusive dick to his girlfriend and soared over the Moral Event Horizon in "Endgame". He's a massive douchebag and later on joined the comic's resident Psycho Rangers which he promptly contributed absolutely nothing too (in fact he was The Millstone 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.
Seasonal Rot: It's commonly pointed out that the post-Endgame stories were this due to the fact that they had intended issue 50 to be the end and when it turned out to still be popular, they were forced into a Post-Script Season, but without their main villain.
So Bad, It's Good: 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 (arguably) just straight up good.
Signature Scene: The "Endgame" story arc, though this has waned over time. It's also famous for cementing the transition to plot-driven stories and killing off the original Robotnik.
Strangled by the Red String: 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 Word of God, echidnas have what is called "the Soultouch" - a Sixth Sense 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.
Strawman Has a Point: 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, 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 (especially keeping in mind she did the exact same thing to Sonic in the Mecha Madness arc and expected Nothing Personal from it).
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.
Straw Utopia: 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 its 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 technologynote For instance, don't make a device designed to siphon huge amounts of Chaos Energy something that the user wears on their body.. 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.
Suetiful All Along: 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 BSODs and 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.
They Just Didn't Care: While the writing may be 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. It must be seen to be believed.
They Wasted a Perfectly Good Character: 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, Ensemble Darkhorse Bean the Dynamite Duck and Bark the Polar Bear were first introduced game-wise in Sonic the Fighters 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 'Tails Adventure, 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. With issue #268, it seems that Ian's reaching back further with the first appearance of Breezie the Hedgehog from Adventures of Sonic the Hedgehog.
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 Snap Back fever. In fact, this became one of the biggest reasons, alongside Pacing Problems, for why even die-hard Ian fans like to hate on the Iron Dominion saga.
The Mecha Sally arc comes off as this to some fans. A lot of it comes from the fact that she never won a fight and some outside circumstance got in the way of her rescue every time. Also not helping is that it only seemed to happen to explain her redesign which could've been easily explained as a result of the first Genesis Wave having residual effects on some people like it did on Naugus.
The introduction of opposing heroic fractions such as members of the Acorn Council. Having characters who call out or cause alternate conflicts for the main Freedom Fighters could have made for an interesting grey dynamic within the team (not to mention serve as potential catharsis by calling out previous shortcomings of characters such as Sonic and Sally). However they are mostly limited to Strawman Political types with Hate Sink personalities, only appearing as a minor frustration in a handful of issues.
The "Freaky Friday" Flip between Sally and Nicole in issue 146 in the story "Circuit Me" is stated as this. A story like this could have explored the birth of Nicole's desire to be more than just an A.I, experiencing real life activities that would eventually give her even more reason for the idea to create her holo-lynx form in Issue 151 "Stargazing" while Sally experiencing(or more precisely)not experiencing what it is like to be a consciousness stuck in a handheld and learning what it is like to be a Freedom Fighter from Nicole's point of view.....only for it to be resolved in a few pages,shafting it as a Noodle Incident.Only at "Stargazing" is this slighty subverted.More details is in here.
The Mecha Sally arc had potential to be better by showcasing the POV of a victim of the Robotizer. Since Uncle Chuck stated that the roboticized are fully aware of their surroundings and what they are doing the whole time as further evidenced by his own robotization, Sally's inner turmoil was never addressed throughout the story. On another note, instead of "Endangered Species" in Issue 243-246, they could have been addressing the fates of the other plot relevant characters instead.More details is in here.
Values Dissonance: 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 Blue and Orange Morality; 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.
The comic utilises not only it's own original cast, but the games and multiple other interpretations. Sonic Universe is devoted largely to giving supporting characters A Day in the Limelight, with the main series itself shifting in and out with Sonic's prominence.
Princess Sally became this in her own mini series. Her role in the main books being largely to play The Straight Man to Sonic, she was left with little chemistry in his absence, leaving her supporting cast to provide most of the conflict and foibles while Sally simply progressed through the mission. Some argue she was still this when she got her own arc in the main comic years later ("Spark of Life"), which similarly relied on several supporting characters and has a somewhat inconsistent mark on her character (eg. being as reckless as she complains Sonic is).