"The Wolverine" won't be rated R. It'll be PG-13 as for it being "really, really, dark" we'll see. The story it is based on has dark elements to it and is very mature, Aronofsky acknowledged the characters dark nature when he was still attached to the project, so I'm expecting this film to be much darker in tone than "X-Men Origins: Wolverine" or even the main "X-Men" films were. I doubt Mangold will want to change things that much. As mentioned a couple of times a rewrite of Chris McQuarrie's script was done by Mark Bombeck, which Mangold stated would be "80 percent intact" and that script has been overwhelmingly praised by everyone who read it. Haven't read any reports about the re-write yet, I doubt we will.