I can't believe people are still discussing this so much. a 23 page thread? I know this would be a great match-up, but all of our speculations, comparisons and arguing really isn't going to change anything. Yes, it is fun to argue sometimes, but getting so serious about it is sort of silly.
I'd imagine that if there ever was a one-on-one between these two Sasuke would win just because it'd be weird for a guy like Neji to do something as important as beating Sasuke. Neji is cool and badass, but he's a 'secondary' character. It'll be interesting to see where these two are after the time-jump (no, i don't read the manga).