I never noticed the gameplay similarities before.
(Incoming ramble about Sonic games ideas, you've been warned.)
Y'know what they should've done? They should've more or less replaced Chip with Ristar, and have the Werehog be you playing as Ristar, rather than being explained as it being Sonic any time it's dark outside. If they had thought of it early enough in, it would've been, like, some slight storyboard changes and making a single character model to replace the Werehog model.
Chip is ... meh, he doesn't seem to do anything genuinely useful. He has plot relevance and unlocks doors and stuff, but it all just seems Aquamanned in for the sake of giving chip a purpose, rather than the other way around. He's like a little kid, he's poorly designed, and his "self-discovery story" is handled in all of like 2 cutscenes, one being "Who am I?" and the other "Oh, I'm this, okay." An utter snooze cruise story-wise too.
Replace Chip with Ristar, and suddenly you have a character who can actually get out there and fight, one whose strengths could plausibly fill Sonic's weaknesses, and one with a bit of a story and characterization to build upon, although admittedly not much. You've got two characters to go around together, Chip is replaced. Ristar is whimsical-like on his own, surely he could be explained to be able to do all the stuff Chip could in a heartbeat.
Dark Gaia seems like the sort of thing that Ristar would be fighting too, y'know? It seems like it could easily be a threat on a cosmic scale if it weren't stopped early on Earth(/Mobius), something where he could be about five star systems away and hear the news, and be like "Oh crap, gotta get over there and stop it!" And then of course he meets up with Sonic and blah blah blah.