Okay, it's time to get something out of the way.
If you want, I'd like you list the characters in Sonic you think are bad(no super forms because they are same character). I'm talking about individual separate entities, and perhaps a brief summary of why you do.
In order of introduction:
The Chaotix in general: Pure filler. Vector had a couple of amusing lines in Heroes, and that's the bulk of what they've contributed to the games. They weren't differentiated from each other terribly well even in their own game, and have no real potential. Espio's got the whole stealth angle, but then when the hell would you ever need stealth in a Sonic game? Better character designs than some of the other additions to the series, though.
Shadow: Dumb design, boring personality, unoriginal abilities. Not awful in contexts where his chaos powers are focused on more heavily, but then that just leads to a more brawling, action-focused gameplay style that doesn't jive with the rest of the series. Has no reason to appear on a regular basis.
RogueRouge: Pointless. Thematically and cosmetically out of place, no unique abilities, and her treasure hunter angle just keeps Nack from ever coming back, who made for a better side villain in a variety of ways. Mostly a backup character for Shadow post-SA2. Having her as a friend in Generations felt exceedingly weird.
Omochao: Kill it with fire.
Cream: Designed as a backup character for Amy and Big, which says it all right there. Continues to exist solely to be cute. When playable, her abilities are redundant with Tails. Is even less plausible as a robot fighter than the rest of the cast.
Silver: Dumb design, awkward gameplay that doesn't fit in with the series, bland personality. His continued presence is a complete and total mystery given how 06's plot wrapped up.
Flawed or limited-use, but not bad:
Amy: Needs better writing, badly. Character design is fine, plot niche is fine, and even her gameplay is periodically interesting, by which I mean she makes Advance 1 tolerable. But they go out of their way to have her be annoying to Sonic, and in turn is annoying to the player as well. Go back to the somewhat toned down, independent personality she had in SA1, please. Current VA is also awful.
Big: Not actually a bad character, just handled badly. He's great comic relief when he's on the sidelines being oblivious to everything around him like the Sonic equivalent of Inspector Gadget (SA1, SatSR journal entries), but terribly uninteresting as a primary character (Heroes, basically everything else).
Omega: If they have to keep a brawler-type character around, at least make it the kickass robot with an amusing love of high ordinance. Makes for a better robot out of control than Metal Sonic's occasional treachery, and he keeps the basic E-series design alive without resurrecting Gamma. I'm also going to quietly ignore all of his appearances outside of Heroes, as should Sega. What the hell were they going for in '06, honestly.
Blaze: Serves as something of a Knuckles alternative, for when dragging him in doesn't make much sense. Being paired up with Silver repeatedly is chipping away at that. Knock it off, Sega. Female representation with a decent design, and it doesn't hurt anything to revisit her setting once in a while. Use sparingly.
The Babylon Rogues: Alien genie birds. Thankfully more or less confined to their own subseries, and even there they've managed to stay hostile instead of switching sides like every other new rivals ever. Won't be missed if they're never seen again, but they're a rare case of Sega showing a little sense in character usage.
Anyone else is either fine (keep Orbot and Cubot forever) or already pretty niche. All of these can hang around in the comics where they don't have to be playable and a good writer can mold them into something likeable.
