Jason Bourne is the clear victor here, he is a killing machine, witness him choking out that dude in a Morocco bathroom if you have any doubts. But in the end, it all comes down to the emotions. Bourne is emotionless. Jack and James they are torn up over their ex lovers. I mean Jack cried at the end of a season and Bond spent an entire movie chasing down the girl's killer, keep in mind this is after he was betrayed by her!
You also gotta realize that Jack and James kill with firearms, while Bourne does not. This is not because he doesn't know how, it's because a gun in his hand is an cop-out. It's like bringing a pencil with the multiplication tables written on it to the time table test in fourth grade, it's weak sauce, you just don't need it.