After rewatching season three, I must say I was quite intrigued by Vaughn whenever his character would get dark. I mean, in season one he was like a perfect little boy scout. And even in season two he was always technically GOOD. I thought it was fun seeing him snap. I loved it when he poured the acid on the Asian torturer guy (from the pilot and season two).
I think the writers should have explored that side of Vaughn a little more. It would have been awesome to see him turn psycho or something. Perhaps, for the sake of his and Sydney's romance, make the psychotic break could have been caused by forces outside of his control? I dunno, I'd love to see him waste someone in cold (or even lukewarm) blood.