I don't think you can really point at a single fighting game and say "This is the best fighting game on the Neo". There are too many good ones.
There are ways to narrow it down though: Do you play by yourself, or with friends. If you play with friends, do they have experience with SNK fighting games, or were they just raised on Capcom (SF2). I think you can see where this is going.
For straight-up SNK love, I kinda like KOF'01 the best, even though everyone rags on it. The graphics are different than all the other ones, but they aren't bad. You're able to adjust how many chars you use and how powerful they are a la MvC2. And, there's a ton of characters to choose from - I think KOF'01 may have the most playable characters of any legit KOF.
There is no greater feeling than letting a Capcom head bring his best fight in SvC and getting pwnt by Terry. Never gets old, either. Power dunk!