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.
Canon Sue: A common complaint concerning Sally. She existed largely as The Straight Man to the main character, and to prove how his trademark "like the wind" ethic was in fact reckless and incompetent compared to her more cautious, meticulous approach. The fact she gradually absorbed spotlight from other characters and thus became the most effective Freedom Fighter didn't really help in this regard.
Complete Monster: Dr. Robotnik, unlike the Affably Evil version of him you'd see in other Sonic cartoons (or the games themselves), is much less pleasant. He is willing to deprive innocent creatures of their free will to get them to work for him, he is willing to turn formerly beautiful communities into severely polluted wastelands, and he doesn't show any remorse for any of this. He turn people into his robotic slaves if they don't obey him, which are quite aware of what's happening to them, and morally objecting to that which their robot bodies are forcing them to do. There are episodes in which some robots are carrying on secret conversations with their loved ones, from before roboticization, only to double over in apparent pain before proceeding to attack said loved ones because of the control Robotnik has over them through said robotic slavery. He even turns the ones who do obey him into robotic slaves.
Creator's Pet: Both Dulcy and Sally were stated to be favorites of Ben Hurst, main writer for most of the second season. They also have a rather "conflicted" reception with the fanbase to say the least.
Designated Protagonist Syndrome: Sonic, though not unpopular in the show per se, gets occasional critism from this. While a fairly effective hero, Sonic is by far the most dysfunctional and arrogant of the Freedom Fighters (Straw Loser Antoine not withstanding), frequently endangering the team due to his cockiness. Many also complain that the goofy Japan-based Sonic seems misplaced in the Americanized dystopian setup, and that the show would have worked as effectively with another Freedom Fighter as the lead rather than trying to tie in to the games series.
Designated Villain: What kind of bad things did Naugus actually do? He didn't do anything seriously bad in the series. Sure, he kidnaps Sally and Bunnie so he could lure Sonic into the Void and then tricks him to get him out of the Void, but wouldn't most people do it if they were trapped in a wasteland for years and then saw the opportunity to get out? He did allow Sonic to take them back after he was out of the Void. And the only one whose life he wants to make difficult is Dr. Robotnik, the Big Bad. The only reason we saw him as a villain was because of Word Of God. Granted, he was supposed to become the next big bad in season 3 but that idea was screwed.
His goal to escape were sympathetic but his methods of escape were somewhat skewed, deceiving the Freedom Fighters by posing as the King, and routinely encasing any one in frozen crystal that becomes a slight annoyance. While just deciding to ditch him and leave him in the Void after explaining his motives may have been a bit callous it may have been slightly justified given he had shown how potentially unstable he was in luring them unwillingly into the Void. As the third season also suggested, his ambitions outside revenge on Robotnik were also yet to be revealed.
It is understandable for him to be how he was. He was trapped in the Void for over 10 years, with only King Maximillian in charge. Plus the aforementioned betrayal by Robotnik. After all that time, it's no wonder he's callous.
It should be noted that the comics adapted from the series very much avert this. Not only does Naugus fully deserve the title of villain, he crosses the Moral Event Horizon many times and is easily the biggest Complete Monster in the series.
One can argue Sonic earnestly refusing to save Antoine from Robotnik in "Hooked On Sonics" (in other words, hating Ant enough to want him to face potential torture and Unwilling Roboticisation) was this to the point of bordering an Out-of-Character Moment (he implied it a couple of other occasions in the series, but in a far more playful and insincere tone to make it fair game).
(Robotnik opens his putrid, rotting mouth wide enough to fit Snively's entire head in for Snively to look down his throat)
Snively(terrified): I... I don't see a heart, sir.
The entire concept of roboticisation in the show. See "Sonic's Nightmare" for the terrifying details.
The robot double from "Sonic and Sally" could very well have been a roboticized Mobian.
The glowing red eyes of Naugus against a black background in the finale.
The Scrappy: Out of the main cast, Dulcy and Antoine are the least liked characters. Say what you want about Sally, but she still has a good amount of fans. Many felt that Dulcy was a pointless addition to the cast, especially since she appeared out of nowhere in the second season and the writers want you to pretend that she there since the beginning of the show. Also, many found her klutzy behavior to be more annoying than funny. Antoine gets a lot of flak for not really doing anything useful. His cowardly personality tends to annoy viewers more than amuse them, especially since he tend to be a Dirty Coward at times. If he was more of a Lovable Coward like Chuckie from Rugrats he probably would have been more liked. It also doesn't help that he really doesn't have any real redeeming traits (outside of a few Jerk with a Heart of Gold moments). Given that he is the Straw Loser of the group and Sonic doesn't like him, it could be intentional.
Suspiciously Similar Song: The orchestral background music certainly sounds familiar... This extends even beyond the show's orchestral theme tune, to the point where the entire score is essentially one big riff on Alan Silvestri's style, complete with harmonies and dissonances based on octatonic scale patterns.
Tear Jerker: Any time Uncle Chuck shows up, expect it to all end in tears.
The scene when Sonic is crying after having to leave his uncle behind, especially after seeing him for the first time in years.
"Blast To The Past part 2" has several, back to back.
Bunnie reverting back to her half-metal body after what turned out to be a temporary de-robotization. She may be Cursed with Awesome, but the palpable pain and sorrow she lets out when she breaks down after changing back, you would have to be completely soulless not to feel.
They Wasted A Perfectly Good Character: Bunnie Rabbot made interesting use of the show's robotocization concept and had kickass cyborg powers to boot. However she had a supporting role in the majority of the first season and was Demoted to Extra in the second, arguably getting the least amount of development time out of the rest of the Freedom Fighters (Rotor and Tails were also heavily Out of Focus for most of the show's later run). The comics adapted from the show utilize her a bit more, but still play her as one of the more minor leads.
Also Tails, who according to Ben Hurst would have got a lot more screen time in Season 3 if it was finished.
Snively for the most part is suggested to be as remorseless and ruthless as Robotnik, still you have to pity the overwhelming amount of abuse he has supposedly suffered from his uncle (who is embarrassed to even acknowledge their relation) for over a decade. The fact the Freedom Fighters often trigger Robotnik's wrath onto him (at one point Sonic seemed to acknowledge and laugh about it) probably gives a valid excuse as to why he isn't sympathetic towards them.