I don't really think it would be a good idea for Rogue to take Ms. Marvel's powers in the movies. It just doesn't seem to fit that character. I think she does need to start being more aggressive with her own powers, but that's another topic alltogether.
I'm still fiddling around with my X5 storyline (heck, I'm still fiddling around with X4, lol.). I'm thinking that about half of the people who took the cure should come down with the Legacy Virus. The other half - including Rogue, Magneto, and Mystique - will have a very mild version of it that goes away quickly and leaves the mutant immune to the virus. Cure patients who get the full-blown illness - called the "Legacy Effect", because it's not yet known to be a virus and instead thought to be a reaction to the Cure - will include a few unknown characters, Illyana Rasputin (Colossus' sister, who will die from it), and Nightcrawler (who will recover). Eventually, non-cured mutants will come down with the virus, and Hank and Moira will discover that it's a virus that can be spread. I haven't decided yet if it should be easy to spread, like a cold; or if it should be something more difficult to spread, like an STD or something. Anyway, the most important non-cured character to get the Legacy Virus would be Pyro (in keeping with the comics).
I'm also trying to figure out how Rogue and Bobby fit into the storyline, given their ties to Pyro in X1 and especially X2. I'm thinking that the virus should move a lot more quickly than in the comics, and quickly leave Pyro bedridden (sp?). Bobby and Rogue will visit him a lot, because they were so close.
In one scene when Pyro's alone with Rogue, he asks her to touch him and kill him, because he can't take the pain and discomfort of the Legacy Virus. She refuses, but he gets her to promise that when he dies, she'll take his powers so he "lives on" in some way. She figures she probably won't even be around when he dies, so she just promised to make him feel better.
Pyro dies a few days later, but is revived by Hank and Moira. When he wakes up, he tells Bobby that he doesn't want to be revived the next time he dies.
When Bobby and Rogue are visiting him together, he dies. Rogue, remembering her promise, grabs his arm. Bobby is about to get Hank, but Rogue convinces him not to. Bobby is appalled by her taking Pyro's powers while he's dying, but she tells him that it's what Pyro wanted. Bobby just stares in shock, until Rogue falls to the floor crying. Bobby runs over to her, takes her hand off of Pyro (it sort of sticks; and when he takes it off, both Pyro's arm and Rogue's hand are bloody), and they hold each other while they both cry.
This creates for Rogue something similar to the comic book storyline where she absorbed Sunfire's powers. Obviously, Sunfire and Pyro have some differences in powers, but they also overlap in parts (such as shooting flames, and the movie version of Pyro could be immune to fire). The powers would eventually fade, though.