Fatal Flaw: The number of times his cockiness had almost gotten him killed...
Flanderization: His originally more playful rivalry towards Antoine evolved into flat out naked contempt (though the lengths of his other traits were usually more a case of Depending on the Writer).
He did however become noticably more cocky and incompetent in the Second Season. More than half the episodes are devoted to him making some sort of error out of recklessness and needing to be bailed out by the rest of the team.
Idiot Hero: Is fairly Book Dumb and often needs Sally's guidance in missions. He has notable showings of resourcefulness however.
Jerk with a Heart of Gold: Sonic can be incredibly arrogant and frequently butts heads with the other Freedom Fighters (usually Sally or Antoine, even if the latter usually deserves it). He is altruistic to a fault however and in his reckless overenthusiasm he is only looking out for others.
Right Way/Wrong Way Pair: Usually the Wrong Way to Sally's more cautious and meticulous approach, especially in Season Two.
Smug Super: To the point some of Robotnik's schemes manipulate his ego.
Small Name, Big Ego: Sonic is genuinely competent and heroic, however he has no problem exaggerating this in his constant bragging, a lot of times actually screwing up missions due to his overconfidence.
You Already Changed The Past: In the time-travel episode "Blast to the Past," it is shown that present-day Sonic is responsible for both the loss of most of Snively's hair and Robotnik's roboticized arm.
Leader of the Freedom Fighters in SatAM and the Archie comics. Based very roughly on "Ricky", the captive squirrel freed from Badniks in the original games (Sonic the Comic used a similar character more akin to her original games counterpart as a minor extra early on).
All There in the Manual: Her surname 'Acorn' is never mentioned in SatAm, though is stated in the show's bible and frequently in the comic books.
Breakout Character: Sally originally had more of a supporting role in earlier episodes. She arguably became as prominent as Sonic himself later on.
By-the-Book Cop: Was constantly trying to keep Sonic in line and endlessly chastised him for taking risks or going outside plans, regardless of whether or not it worked. Whether or not this was justified varied (especially in the second season, where Sonic made increasing fumbles and put the team in danger). She had her own careless bouts at times however.
Early-Installment Weirdness: While her personality is largely the same, the pilot's version of Sally has a pink color scheme (with black hair) and a higher more childlike voice. This design would be used in initial comics as well, which initially used early concept work for the show to develop upon.
Foil: Largely to Sonic, her meticulous and cautious personality contrasting Sonic's spontaneous and reckless persona. Both share a similar arrogance and ego that only fuels their bickering more. Also to Bunnie, but less so.
Flanderization: He was originally rather pompous and cowardly, but had some amount of lucidity and nobility. By Season Two however he is more or less a full time Straw Loser for Sonic, barely able to spend five seconds without saying or doing something stupid or narcissistic and acting like a full blown Dirty Coward.
Freak Out: Antoine has one hell of a freakout in "The Odd Couple" where he is forced to share his house with Sonic for a night.
Ambiguous Disorder: Well, as much as they could get away with in a kids show, but Rotor prefers being alone and spends a little too much time on his niche, inventing things. His vocal inflections and overall social behavior are somewhat off as well.
Art Evolution: While several other characters go through minor design changes, Rotor's are most evident, gradually becoming chubbier and more anthropomorphic. He goes through at least two drastic design changes throughout the show's run (once after the pilot, another during the second season).
Early-Installment Weirdness: Rotor has a goofier design with a purple color scheme in the pilot episode. Similar to the Sally example this would be utilized in the comics (though actually was kept as his permanent design in that media). His design would be changed again halfway through the show's run.
Nice Job Breaking It, Hero: He was the original inventor of the roboticizer, which was made to help old people live longer. Unfortunately, it had a side effect of wiping their minds clean and they had no will of their own, which is why Robotnik stole the idea from Chuck after he thought he destroyed the blueprints for it.
The Big Bad, responsible for overthrowing the king of Mobotropolis, and converting the city into a heavily industrialized center. He rules with an iron fist, roboticizing the entire populace in order to quell any and all rebellion.
Axe Crazy: Can be this at times, mostly in the second season.
Bad Ass: This Robotnik is one of the few incarnations to have actually taken over the world! That alone is pretty badass in it's own right but this incarnation practically turns it up to eleven by also giving him a baritone voice, an even more badass mustache, a pair of black red eyes, and tops it off by making him half-cyborg!
In Name Only: There are about 5 similarities that this Robotnik has with his game counterpart. His name, the fact that he uses robots to conquer things, that he turns animals into robots, his Badass Mustache, and the colors of his wardrobe. Remove his name and wardrobe coloring and this man would be a completely separate character.
Would have been subverted for the Third Season, where he would have been revealed to have survived the explosion and got teleported into the Void.
Knight of Cerebus: Unlike most other counterparts of the doctor, Robotnik's actions are depicted in a far more serious and sinister light, especially compared to his nephew. Lightened in the second season, where he gains more comical fluctuations, and we are introduced to an entity that makes even him cower in fear.
Large Ham: While not as extreme as his previous incarnation, this Robotnik was still pretty hammy, with his heavy breathing, low voice, and long pauses. Though these qualities were mostly present in the second season.
Stupid Evil: More so in Season 2. While in his past he was able to make lengthened charades to maintain his plans for power, by Season Two, Robotnik just can't resist Kicking The Dog at the most inappropriate time.
Ineffectual Sympathetic Villain: Snively a treacherous weasel whose ruthlessness only pales compared to his uncle. However in action he is pitiful bumbling coward that Sonic and even the highly cautious Sally have problems viewing as a serious threat.
Laughably Evil: Not much more pleasant than Robotnik, though far more blundering and goofy.
Not-So-Harmless Villain: While often seen as far more pathetic than Robotnik by the Freedom Fighters, he actually gotten closer to discovering and conquering Knothole than his uncle did. In the planned Third Season he would have briefly took control of Robotropolis, though would lose control later on.
Servile Snarker: Often makes snide remarks about his uncle behind his back, especially in Season 2.
The Starscream: He constantly grumbles over having to serve the Doctor, but doesn't actually attempt to harm him. By the Second Season he has blatantly come to resent his uncle's abuse and makes a few shrewd plans behind his back (he once attempted an attack on Knothole while Robotnik was gone, as well as making alterations to his base that would ultimately save his life when it was destroyed). He simply plays along until Robotnik is electrocuted in the final episode, then is seen donning his uncle's trademark yellow cape. He does, however, resemble Starscream in voice, especially considering his voice is done by Charlie Adler.
You Have Failed Me: Robotnik attempts this indirectly in "The Doomsday Project", leaving him to die in his imploding base out of spite. Snively however had predicted as much from his uncle and had made his own methods of escape.
Robotnik: Only room for one, Snively! *closes escape pod*
Sealed Evil in a Can: In both SatAM and the comics, Naugus spent years trapped in the Void/Zone of Silence (the name depends on the continuity). In the comics, he escaped and was resealed several times before escaping permanently.