Well...
Homing Attack, Lightdash, and Analog control are turned on by default.
Knuckles gains multiability.
Tails' flight works more like in SA1.
A very faint, hard to notice sound effect when you land.
I remember seeing something in the source code about turning down gravity, but it might've just been my imagination.
If an object with MF_BOSS is in the level somewhere, the camera will lock onto it. (The only time Analog control ISN'T a piece of crap.)
Player hits his "falling" frames when you simply drop off a cliff.
Might be a few other things, but that's all I know.
Edit: Curse you Sonicmaster.