I had both and still own a Japanese Mega Drive to this day. I just have greater memories of enjoyment on the Mega Drive, not to say the SNES was not a great machine, because it was. I think mainly because the Mega Drive was released earlier then the SNES in the UK, and I remember being blown away by the superb graphics of Super Shinobi, and arcade ports of Golden Axe, Ghouls 'n Ghosts and other exquisite offerings like, Ghostbusters and Super Monaco GP. Of course Phantasy Star II was a real favourite of mine back then. I have to mention the YM2612 too, what a chip! Music to my ears. I have quite of a few of those video game soundtracks on my iPod.
As for the SNES, all I can remember is hours playing Smash T.V., Mortal Kombat and endless Street Fighter. Juster fighters really, but of all of them, a personal favourite was Ranma 1/2 neighbourhood combat, a real gem of a game.