Despite the dire cameras, it's not really the 2D/3D thing that has doomed Sonic.
The problem is that he doesn't move right. Controlling Sonic is an exercise in frustration and annoyance, because he moves and accelerates so fast that you get little to no precision in control. It's almost impossible to make sure that he lands in a particular spot, and when things are at their worst, he'll land running at full speed no matter how fast you were running when you jumped (Sonic 2006 is fond of this), meaning that you go flying off the platform you just jumped to. It's also hard to line up for a jump, because even slight inputs produce large effects.
Precise control of the character is the core of a platforming game. Sonic games don't have it any more, and just returning them to a 2D plane does not resolve that issue, as Sonic Unleashed is quick to show, the actual Sonic levels are still shitty because of your shitty control of the character. (and their unimaginative linear level design, but that's another problem)