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.
Likewise, no matter how much you hated Chris, that final scene with him in Memories of the Wind is pretty damn tear-jerking, especially for anyone who's had to let go of their best friend before.
Ass Pull: The justification and execution of why Sonic and company had to go home at the end of the second season was... rather poorly written. Chris's damning lack of judgement in that episode does a very good job of distracting the audience from the gaping plot holes, however.
Character Rerailment: The comics adaptation does well to reverse some of the Flanderization prominent in the anime. Sonic in particular was back in main focus and regained a lot of his original more emotive personality, he and Tails also work together on a more frequent basis.
Crazy Awesome: Dr. Robotnik in the comics. Especially after he takes up the title of EL GRAN GORDO!
Chris Thorndyke: not liked by many fans, yet appears in 99% of the episodes to the point where, in the first series, he gets considerably more screen time than the title character. Also characters repeatedly tell us just how great Chris is, you know, just encase somebody didn't quite realize.
While Chris is almost universally hated, a number of the other human characters are quite popular among fans such as Topaz and Mr. Tanaka.
Fridge Horror: At the end of the third season after Cosmo sacrifices herself, the seeds of her species are spread across the galaxy. Now then, take into account that we don't see where most of them land. In fact, we don't see where any of them land. Let's also take into account that it was shown that Cosmo Grew from a seed into a small baby. This means That all of Cosmo's seedling would develop into babies. Some of them would develop in the wild, without any civilization.
Growing the Beard: It didn't occur that much, but the Metarex season was somewhat better because they expanded on the actual main characters, whereas most of the first seasons Chris stole the show from the main characters. In the Metarex arc even he became less annoying.
Guess what other infamous Sonic-related series involves an OC named Chris who takes up 99% more screentime than the title character?
Eggman's insistence about being the show's real protagonist in the original Japanese version of the "Eggman Corporation" two parter only becomes more amusing due to the comic series, where he more or less does become the Villain Protagonist.
Magnificent Bastard: Luke/Lucas/Dark Oak. His objective to turn the entire universe into one with peace and tranquility and devoid of flesh and blood so that plants can rule is motivated by his love for Hertia/Earthia, and he uses carefully-laid-out plans and strategies to carry out said objective. Even though he acts like a monster sometimes, deep down, he's rarely cruel and is actually troubled by his past. His smooth operations mainly involve collecting the Planet Eggs as well as the seven Chaos Emeralds, and for good reasons, and not to mention, there's also his act of manipulating Cosmo into using Sonic and the others to collect the Emeralds for him so he could claim them with her help. In the end, following Cosmo's Heroic Sacrifice, he reforms and finally realizes the errors of his ways, and happily departs for the afterlife alongside a vision of Hertia.
Black Narcissus shows that he truly crosses the line when he captures and tortures Chris and Cosmo and uses them as bait to have the Metarex prototypes Silver and Gold test Sonic's speed, strength, and skills. This moment is what triggered Sonic's Unstoppable Rage and Superpowered Evil Side transformation, and this action was just enough for Narcissus to cross the horizon itself. Good thing Eggman and his followers came to help calm things down — after all, Even Evil Has Standards.
Dr. Eggman: (to Black Narcissus) It's one thing to take them prisoner and threaten them but when you actually hurt somebody, that's going too far.
Pale Bay Leaf crossed the line with what he did to Leon and several other anti-Metarex resistance pilots from Molly's home planet: embedding their bodies into the bases of trees and leaving them to weaken within there as a show of betraying them after promising them fame and fortune by inviting them to the side of the Metarex.
Averted with the old man who, in his youth gunned down a twelve year old girl on board Space Colony Ark. Decades later he's clearly deeply remorseful for what he did, and gives Scarlet the information she needs to finally understand what happened to her father all those years ago.
One-Scene Wonder: Dark Super Sonic. He's on screen for under a minute he's arguably the most popular thing added in the show.
Rescued from the Scrappy Heap: Chris in the Metarex arc. Partly by giving him less screen time, and making the time he did have on screen actually productive.
Strangled by the Red String: One can't help but feel this way about Tails and Cosmo's relationship in season three. There's really no reason why Tails fell for Cosmo so suddenly, or why Cosmo was paired up with Tails instead of any of the other (and older) males on the Blue Typhoon. And this pairing was strangled together even in-universe. In one particular episode, the Chaotix try several methods to pair the two together. They do this because...um......well, uh......BECAUSE!
In another episode, Vector claims that Cream, a six year old, should be sent home to her mother rather than tagging along with Sonic and the others around the universe fighting a powerful and murderous alien force. While he steps over the line by trying to send her back by force, it's hard not to feel he has a strong point, especially since Cream shows far less physical capability in this interpretation. It's only worsened since, much like their arguments with Knuckles, the other team mates are belittling to his theories and angrily label him an egotist who should butt out.
Take That, Scrappy!: Eggman delivers an awesome one to Chris in episode 49. He lies on purpose about his involvement in the time freezing issue just to see Chris' reaction to his admittance in order to gauge his selfishness. Then when Chris starts bitching about being lied to when Eggman admits that he was lying just to see said reaction, Eggman starts delivering the home truths about how he is so willing to scapegoat someone else (Him) just for the sake of having a reason to keep Sonic all to himself. Many Chris haters cheered at this verbal smackdown and it cannot be denied that this moment was one of Eggman's greatest Moments of Awesome in the entire series.
Unpopular Popular Character: In universe, Eggman and Knuckles are both Butt Monkeys intensely jealous of Sonic's popularity. Out universe they have almost as big a fanbase as the latter (though granted this was also before the show made them 'unpopular').