Every script does go through revisions yes and most likely McQuarrie's would have or will as well but from what was posted on the plot a few pages ago and what little we know so far I'm inclined to suggest that "The Wolverine" will be the film that fans were anticipating with "X-Men Origins: Wolverine". Another reason I think Fox injected all of those mutant cameos was maybe because they were testing to see how well fans responded to them. We know a "Deadpool" film is on the way that won't use the version of the character that Wolverine used. I believe that "Gambit" script was written or at least considered. A new version of Emma Frost (the proper version it would seem) is being used in "X-Men: First Class".
All I know is that when Aronfosky's name was being bandied about my interest level went through the roof.