Add me to the list of folks that prefer Mortal Kombat (and in fact, almost all multiplatform releases) on the Genesis. One thing that I haven't seen mentioned though, is the control. The Genesis version arguably looks pretty darn rough compared to the SNES, with its screwy, unfinished-looking health bars, and what appear to be smaller sprites (though I have heard some argue that the SNES version's are "too big"; I don't know).
Anyway, being a huge fan of the original arcade game during its heyday, I always felt the controls in MK on the Genesis were waaaayy tighter than the SNES. The Nintendo version seemed to me to suffer from some sort of lag or slop in its movement. I also think the controls failed to capture the "feel" of the arcade.
Allow me to go off on a tangent here...
I find it interesting that so many people seem to prefer the music of the SNES vs. the Genesis. To me, the SNES sounds like a generic General MIDI wavetable synth, while the Genesis is almost always just straight-up FM synth goodness. The downfall for a lot of Genesis games' music was that developers were most often using the synthesizer to generate realistic sounds, which, beyond some drums, strings, bass and electric piano, were never the Genesis' strong suit. Don't get me wrong, I love a little Road Rash wanky guitar now and then, but to be honest, it's a horrible emulation.
Folks who knew how to play to the Genesis' strengths (like Yuzo Koshiro) and produced full-on synth music were able to squeeze some shockingly amazing stuff from such a simple machine. YK in particular was tweaking the operators to sound like filtered 303s, DX7 basslines, and, unless it was samples (and hooray if it was), 909 drums that are almost picture perfect!
Okay, I veered a bit off-topic there, but when am I going to remember to post that again?