Back when The Wolverine was in early production, and director James Mangold wasn't saying much, fans only had speculation, old comics and a few randomly-selected photos of Hugh Jackman as Logan to work from--and the result was that many assumed it would be a "flashback" film set between the events of X-Men Origins: Wolverine and the first X-Men film, in which Logan encounters Rogue, Professor X and the rest of the team.
That speculation wouldn't have been there if one of the co-writers had beeen able to work out some details and convince everybody to do what he originally wanted for The Wolverine: to incorporate Rogue in a big way.
"I love Rogue and I just think that there’s something about this idea that Rogue is tremendously empathetic but incapable of safe human contact," Mark Bomback told Creative Screenwriting. "That always moved me and I thought that’s what really got to the heart of what makes the X-Men franchise so unique. So I was trying to do something with Rogue in the script. I even had a set of ideas that the old man possessed a version of Rogue’s power and that was going to be indicated by a white stripe in his hair. Eventually it became very goofy, and I threw it out because I started realizing throughout the script that it became more problematic than cool."
He added, "It’s no accident to me that in the first X-Men film the first two mutants that you really see who have a connection are Wolverine and Rogue. There’s something special between them, so I was trying to bring Rogue into it, but it just didn’t get there. I regretted there wasn’t a way to figure it out, but when I look at the film now, it would have stuck out if we tried to shoehorn her in there just because it was another character from the universe."