Polygon has the hot scoop in an article entitled Aladdin designer Shinji Mikami on why the Genesis version is better
Shinji Mikami, known for his work on famed games like Resident Evil, Viewtiful Joe, and Phoenix Wright: Ace Attorney, has pledged his support for the Genesis:
"If I didn't actually make [the SNES game], I would probably buy the Genesis one," Mikami told Polygon in an interview. "Animation-wise, I think the Genesis version's better. The Genesis version had a sword, actually. I wanted to have a sword."
Blast Processing > Mode 7 any day of the week. (I agree with Jeff, and think the music is better on the Genesis too.) Sorry if this is a flame post.