What I reckon will happen in X4 is that the cure turns out to be lethal in some cases and Rogue finds out shes's dying. This would have such an emotional impact on the team paralleling cancer today and how some people are forced to watch their loved ones fade away. However, there is a solution to this 'Legacy Virus' and that is the anti-cure. Rogue has a choice slowly die and never be able to see Bobby again or regain her mutant abilities and face the problem of never being able to touch people. I believe she will choose to accept her mutancy after realising who she is but something goes wrong with the anti-cure and it ends up transferring more power than she had before e.g. flying, super strength. Hence the Rogue we all know and love is created. This could be a way of futhur expanding the character's powers such as Mystique. I think the only reason Magneto wasn't as affected as the others is because of how powerful he is but I have a feeling that he has been used enough as a villain so he should join the X-men when they are forced to fight against a new foe in X4: ReEvolution :P!