2D and 3D fighters together? Sacrilege! My deciding factor for deciding which is the 'best' is the one that displays balance, depth and control at a very high level. Thus, the absolute best fighters in each genre are:

Best 3-D Fighter: Virtua Fighter (not Virtual). No contest. You all really need to give Virtua Fighter a serious effort. Games like Tekken and Soul Calibur allow you to get really really good with many characters, but VF takes a commitment to one character to learn all of their ins and outs. You can still use other characters, but the amount of time it takes to 'master' one character in VF is substantially more in-depth than any other game. And it pays off once you do.

Best 2-D Fighter: Street Fighter. Despite the fact that my avatar and sig is a character from KOF (which isn't on the list, though I guess it could be grouped under Fatal Fury), I'd still pick SF as the top 2D. Guilty Gear is awesome, but SF still edges it out.

For the poll though, I picked VF.