Another solution I suggest is simply making the robots bigger. In 3D space, due to the size of most of the robots, it's hard to simply jump on them with precision (try playing Unleashed without homing attack).

It's not like Sonic Team hasn't showcased the size of the robots in 3D space before: http://www.youtube.com/watch?v=BZB6uMCkVL0

This would allow the extinction of the homing attack, and the variety of the bots in which they once had.