It would seem to me that for whatever reason, the Sonic series just hasn't been able to transition to 3D. What is it that makes it so difficult compared to most other franchises?
The reason Mario works is because from the very beginning, Mario has been about exploring a stage. That means jumping on platforms, hitting obstacles and such. It is all about careful exploration of your surroundings. Hence why it translated well into 3D because you are basically doing that but in another dimension. But note this has problems as now they have a camera to deal with, which can mess up with your perspective, especially when jumping and exploring.
Sonic's concept relies on speed. Yes, you can stop and explore levels, but Sonic's main appeal is that he is really fast. This can work better on a 2D plane because you are just moving left and right. In a 3D space, however, you have far more directions to traverse through, and thus when you control Sonic at high speeds you have to control him, and that will become hard. The camera will get stuck and Sonic will crash onto objects.
This is why it has taken Sega many years to try and perfect this.