At any rate, the games and comics offer no substance whatsoever. The former in particular are largely some of the worst professional attempts at storytelling that I have ever seen, largely because the characters are so shallow and unlikable.
Well not to keep disagreeing but unfortunately you're wrong there as well. Shadow and Rouge both have much more interesting and in depth personalities and backstories than either Bunnie or Rotor in SatAM (heck, Chris Thorndyke is a much more developed character than either Bunnie or Rotor). Now this could be argued that they would have gotten more screen time in Season 3, but there is also just as much chance as they wouldn't have. Nothing about Season 3 was set in stone, so there is no guarantee either would have had more panel time.
On top of that, Bunnie and Rotor's likability comes from the fact they are "nice". That's all they got going for them. Sure Rotor is a tech head and Bunnie is a Southern Bell, but beyond that they don't do anything more than be a named Background character. They aren't really more likable but rather so underused that you have no reason to dislike them (Unless you include Rotor making Robecca in which case Rotor is more dislikable than Robotnik 
)
Antoine's personality on the other hand, was also reduced to be the buttmonkey of everyone else in season 2 as well. Honestly if I were any of the other Freedom Fighters, I'd have Ant pulled from the team as he is so useless he's more of a hindrance than a benefit. In Season 1 he's at least charming and while cowardly he has good intentions and is willing to face his fears for the benefit of his love, Princess Sally. By Season 2 that was replaced that he's pretty much just cowardly, the butt of everyone's jokes, and useless. He's like the Dr. Smith (Lost in Space) of SatAM....only Doctor Smith was likable because he was a pompous windbag with no redeeming qualities, Ant is supposed be liked but has no reason for anyone to do so.
Again I'm not disliking these characters, but rather saying the games and the comics aren't "Worse" then SatAM there just a different style of taste. It's like comparing chocolate pie to chocolate cake. You can like one over the other, but it's not because one is better, it's just your personal taste.
Production-wise, yeah, it's a major flub. But I do have an in-universe theory as to why nearly everything was different during the second season:
Since King Acorn was reported to have been seen in "Sonic Boom", this suggests that he managed to escape Robotnik's coup upon being dethroned. If so, it's possible that Sonic and Sally's time-traveling adventure in "Blast to the Past" resulted in a paradox in which Robotnik succeeded in capturing the King and banished him into the Void. This could explain why Sally had a more important role during the second season (having to take her "late" father's place), and why Antoine was an even bigger coward than before.
This would explain things, but as you said it is a in-universe theory, not actually the production.
It's also the best explanation. I also like to think that act explains why in season 2 both Robotnik and Snively are less stable. In Season 1 Snively isn't as wild or crazy, and Robotnik tends to be more calm and collected, only showing his rage when he loses. In Season 2 Robotnik seems more obsessed with defeating Sonic than the other Freedom Fighters, and Snively varies from being a bumbling idiot to being chaotically dangerous.
Didnt we learn about how bad Time Paradoxes can be from Back to the Future II
No, because the first and third both say it is okay to change History into our favor.
In 1 nobody really cares Marty made his family successful, and 3 revolves around Marty going to the past to avoid Doc being killed, just because he doesn't want Doc to be.
