As you might remember McQuarrie is no stranger to the X-Men universe, having originally penned the first X-Men script before David Hayter came in. A very brief Google search doesn't reveal what McQuarrie's script would have been like, so maybe someone else can offer up what might have been. I think I can safely say that if he had written Origins, there wouldn't have been gaping continuity errors and laughable memory-removal MacGuffins.
Like most Wolverine fans, I love Frank Miller's Japan saga. It's the first time Wolverine was actually shown to have those things called "feelings," experienced something known as "failure," and it deepened his character beyond the berserker who did nothing more than hack, slash, and hit on Jean Grey. If done right, we could honestly pretend Origins never happened, and this is Wolverine's cinematic origin story.