Frankly, this sounds like a terrible idea. Having separate paths for all 3 characters makes it nigh impossible to balance between them, not to mention 2D mode's horrible physics and even MORE Thokfest qualities. That, and you completely ignore 2D's strength: The ability to do scenery without worrying about the player crawling over it and breaking the level. I see none of that here, but I'll give the benefit of the doubt and say that you haven't gotten to that yet.
Frankly, I see NO reason to make individual paths for the 3 character types a good idea at all, as it just takes away something from race; it's like two players are on two completely different levels. It's not like you can't NOT put the same characters on the same plane. It's probably possible to balance them if you try to nerf Sonic's abilities here and there with obstacles to give Tails & Knux something against Thokfests. Though, given how Sonic is supposed to be THE fastest and has the ability to reach top speed with a double jump, it would be quite difficult, multi-plane or not.
I still wish SRB2 Riders could be ported...