My ideas would be more along the lines of Robotnik-piloted machines (like the main bosses from to S3&K). The concepts are the important part, and if used it would be easy to design an enemy other than Eggman to carry out the fight.
My first idea is a platformer boss. The camera would be stuck on Eggman so you're always facing towards him. He flies up high and shoots down spikes at Sonic. Sonic dodges them and they plant into the ground leaving their dull sides exposed. Each spike is longer than the last one. Finally, when none are left Eggman (with a giant spike on the bottom of the machine) rams down at a final attempt to hit Sonic. After dodging, Sonic jumps up the spikes (from shortest to longest obviously) until he can reach and attack Eggman. After being hit, the spikes either all gather from the ground and re-attach to the Egg Driver, or (if used in the Crystal Frost, which the spikes would be made of ice) shatter and new ones would form on the Egg Driver
Increased Difficulty (pick and choose): Spikes stay down for shorter periods of time, Eggman gains a close range attack once planted, spikes launch from the ground shortly after being stepped on, etc.
Sorry I'm no visual artist.
This is a chase boss. Think of it as a combination of a chasing boss (Like Eggman in the Metal Sonic fight in SCD) with the 2nd boss of Sonic The Hedgehog (16-bit, Marble Zone) where you're running from him and he's lighting the floor behind you on fire constantly. The camera is behind Sonic facing forward (away from the boss). You run on a wide path staying ahead of the boss. At certain intervals, an elevated path will appear on one side of the track. Steering toward and jumping onto the path puts you underneath the track (upside-down) but the fire is still a hazard. Another path similar will show up, successfully getting on it puts you on the offense by getting above the boss for a hit. Missing the second path forces you onto the top-side of the track again.
Increased Difficulty (pick and choose): The boss starts using projectiles during the fight in attempt to force Sonic to steer from the elevated pathways, gains a large projectile that automatically hits should Sonic fail to reach the elevated pathway on time, etc.
I'm redoing these concepts into bosses shown in the Yasuhara Hirokazu sketches for the levels. I've already finished adapting the Egg Incinerator into a Dragon Boss and now will continue working on concepts.
If possible, there could be a gauntlet boss at the end where Robotnik sets up fights similar to the bosses fought throughout the game (similar to Sonic 4 E1). Dragon II (in the concept for Candy Mountain) could probably fit with the Driver concept.
I just realized my Incinerator is very similar to synchronizer's second concept. This was completely unintentional.