Obvious differences include:
- Cutscene of Robotnik looking at his monitor as Sonic advances through the game, a la SegaSonic Arcade
- Mobius loop in the Toxic Caves minecart
- Different sprites on the wall of the steam room in Lava Powerhouse
- Robo-boiler boss layout slightly different, background very different. It looks almost like it was originally going to be in The Machine Zone.
- Different scoreboard graphics in the bonus stages
And there are probably other differences that I didn't notice. Start video dissection immediately!