Season 2 while it seemed to get a better handle on making the characters act smarter it brought character assassination to the bumbling Antoine. Dim, but useful in season 1 becomes nothing but a self parody of himself and brings nothing new despite being given two episodes dedicated solely to him. Robotnik's sinister nature is toned down for him to be more sarcastic and dry, with much of his menace removed becoming rather similar to the Underground version.
I can question that. Season Two didn't so much keep the characters consistent to me as much as it did just Flanderise them. Sonic in particular just became non stop reckless and obnoxious, losing a lot of his on-the-fly resourcefulness just to make Sally's strategic skills look better. Sally in turn lost a lot of her flawed side and fallible moments in favour of just being 'rightfully self righteous' (no one likes a character with an ego who NEVER has it bite them back). Antoine was simplified to be even more idiotic just so Sonic would look comparatively better, and even that backfired since Sonic's rivalry turned into more a contemptuous jock, the only time Sonic was excessively spiteful towards Ant in Season One was 'Hooked on Sonic', otherwise he was just a playful troll to Ant's snobbishness, while Season 2 there method of making Sonic look 'better' than Ant was the former non stop in-your-face snarling to the audience 'Eeewww, check out this loser, isn't he annoying? Aren't I WAYYYY cooler?'. Even with Ant's almost lack of redeeming qualities, he was now so pitiful and dumb against Sonic's naked schoolyard bullying of him that I still felt sorry for him.
The rest of the cast barely existed. Rotor couldn't compete with Antoine's oafish qualities so just became a bland techie with no quirks of his own, while Bunnie became completely inactive so they could limelight Sonic and Sally's 'dream team' dynamic non-stop. Any other Freedom Fighters like Lupe and the Wolf Pack felt pointless for similar reasons, while in Season One they at least tried to make some of the supporting cast matter, despite them being one shots.
I didn't mind Robotnik gaining a clownish more emotive side, but alongside it came an excessively arrogant and 'evil to a fault' approach to his villainy. While Season One Robotnik was chillingly savvy and pragmatic, and at least themed his evil on his love of robotics (hence his genuine affection for Cluck) Season Two Robotnik was evil for the sake of being evil, and often themed around cliches like 'I must backstab every cohort BEFORE I've won and then place them in easily escapable long running booby traps so I can watch them suffer', which also had the ill fated side effect of making many of the Freedom Fighters' victories based more on the villains' stupidity than their own competence and making a lot of the premise run too much on suspension of disbelief, I couldn't buy this character keeping control for a decade (seriously what was to stop Sonic hauling him to jail in Sonic Conversation?).
The benefits of Season One was that with multiple writers, they all made different attempts at experimenting with the cast, no consistent favourite was made and they tried to fill in the gaps the others didn't. Indeed it wasn't always that consistent, but not to the extreme it couldn't be seen as the character in a different light. Season Two had an okay idea having Sonic screw up and get an ego check once in a while, but then they did it OVER AND OVER, and didn't balance it out with any role reversals like Season One had, which felt like the opposite extreme.
Season Two had the benefit of continuity, but little of it was used for character development. Some like Tails and Chuck stepped up to be more proactive (even if Tails got, what, ONE episode?), and dynamics were tweaked like Snively being retooled to loathe Robotnik, but their actual personalities mostly felt static, something that wouldn't have been so bad if a lot of them hadn't suffered a lot of decay from Season One (and even in that season some could have offered a lot more).
I will grant some of Season Two did feel a lot more character-driven than Season One regardless, but it felt mostly in the form of either comic relief or idiot balls to enable the opposing side to preside. Flaw based screw ups work for humanising characters, but overdone for the sake of plot devices it becomes cheap and repetitive, especially when done with the same one or two characters over and over (Sonic or Robotnik getting overconfident, Antoine or Snively being bumbling....and that's about it, unless you count the unbelievably dumb way King Acorn and Chuck assisted Robotnik's rise to power).