This is another match-up where it's tough to choose. I'd say it's the toughest yet.
I really like both controllers a lot. The Genesis 6-button controller has a better directional joypad, a more comfortable feel overall, and the 6 face buttons come in really handy for fighting games. The SNES pad isn't as good for fighting games, but having the two triggers at the fingertips meant that it was relatively easier to press three or even four buttons at once.
This is the type of thing that makes me wish there was a controller like the Genesis 6-button controller, but with the addition of triggers like the SNES. Oh wait, there is--it's called the Saturn controller.
I agree with kisrael, the SNES pad really contributed to the concept of controller design by introducing the triggers. I'm really inclined to choose the SNES for that reason...but, at the end of the day, I think I'd still really rather have the Genesis 6-button controller, triggers or no triggers.
So, after giving it much thought, I carefully cast my ballot for the Genesis 6-button controller.