Okay, here's what I know in terms of differences between versions:
The PC (and therefore Gems) versions have several glitches patched. Running over the tops of levels is pretty much gone, although the thru-the-wall trick used in MM2 is still there. A spring in MM2 Past has been moved up a few pixels in the PC and Gems games, allowing MM2 Past to be a completable level (somehow, the word of the incompleteable level spread from the Mega CD game when it shouldn't have). The Japanese Mega CD version, Japanese Gems version, and PC version with an edited .ini and a custom soundtrack support the Japanese songs; all other versions have the American songs. The robots you noticed might be a difference between time periods, because I don't think any object behaviors were changed (this is Sonic Team, you really think'd they'd take the time to change things for a second release?). The speed shoe and peel out differences are likely because the emulator's running at a different speed than you're used to; again, I can't imagine that being changed.
If anybody begs to differ, PLEASE correct me so that I can TA any altered versions.