Neo Geo hands down. What alot of people seem to forget is the fact that Neo Geo was way ahead of its time. Yea SNES was a good system but Neo Geo was a powerhouse as the only console that offered true arcade graphics and gameplay. The Fatal Fury, Art of Fighting, King of Fighters, Bust -a-Move, Sengoku series were all huge with out of this world gameplay. Lets not even start with Metal Slug. Neo Geo's failure was due to the super high price point at the time. Didn't it cost about as much as the PS3 did at launch? SNES was simply established because of the nintendo brand, but far inferior to Neo Geo. Genesis had several unappreciated gems like Kid Chameleon (which I think is better than any Mario except for my favorite Mario which was 3 in which case I declare a tie).
SNES seemed to have a graphical edge over the Genesis when you compare games like MK2 on both systems for example. Turbo Graphix 16 had a gem in Bonk which was massively underappreciated. I feel SNES fed off its established brand popularity as opposed to the far superior games Neo Geo had. In fact Nintendo's dominance was only crushed with Sony's 2 systems which is unprecedented and amazing when you consider how well established Nintendo became. Looking at things objectively Neo Geo was the superior system plagued by being the new kid in the market with a super high price point.