Wow, I'm surprised by the negative opinion of the Genesis around here. People seem to champion the strengths of the SNES while only focusing on the weaknesses of the Genesis. There's no point talking about how practical a Genesis port of SFA2 would've been, the reason it wasn't released was because it wasn't worthwhile at the time.
As far as how well the Genesis could handle a port, it could be pretty damn good on cart. The Sega-CD is out of the question because of the limited ram. The amount of animation in a cart port would only be limited to the amount of storage given, whether it be straight memory, compression or whatever. If many factors at the time were different and an otherwise practical port
was put out, I think that it would've been fine to have cut a bunch of characters and maybe a few more stages in order to keep the animation decent. Didn't Alpha 1 have less stages than characters?
Basically the Genesis can do almost any 2D fighter, only extreme things like full screen zooming or screen filling sprites would need to be cut. A benefit that a Genesis port would have over the SNES port is it could be pixel for pixel in the 320 wide mode. The perspective would still be off compared to the arcade, but it was the same for lots of 16-bit home ports.
On-screen color wouldn't be an issue the same way it was in the SFII ports. The Alpha/Zero sprites aren't shaded like the SFII series sprites. They're two-toned with colored lining. The drabber backgrounds are also Genesis-friendly and wouldn't look as out of place with repeated color.
I think that this example is on the conservative side of what could be done-
http://members.shaw.ca/black_mustard/sfa2_genesis2.png
The only 16-bit console port that wouldn't have been much of a stretch had Capcom allowed it to happen would've been for PC Engine Arcade Card CD.