I had a SNES when I was a kid so I was clearly biased and thought it was better. Looking back now with no attachment at all to Nintendo and Sega, I still say SNES was better. The RPGs are the difference for me. As awesome as Shining Force 2 was, it cannot compete with Final Fantasy 6, Chrono Trigger, Secret of Mana, Earthbound, etc.
I like fighting games too and both Street Fighter 2 and Mortal Kombat 2 were better on the SNES. Genesis had the better MK1 though (mostly due to actually having blood).