Graphically the Sega Cd and Genesis are almost identical. The CD version simply has some minor things the cart doesn't, aside from cd music.
The cd has that FMV intro, that uses some footage from the tv commercial.
The intro bio FMV of each other characters, opposed to static screen on cart, but its only a second long.
I think the stage that had Shang Tsung sitting in chair had him clapping at the end of the round, which I don't think was animated on Genesis?
The spike pit is graphic, with heads on on the spikes, as opposed to nothing being down there on cart version.
The only real down side is the extreme loading times, wait till Endurance Rounds, otherwise the game is the exact same thing.