You know an idea that kind of excites me, that I think they may go with? So in the beginning of The Last Stand, we have the wonderful most hated scene where a younger version of Magneto and a younger walking version of Professor X are walking to go meet with young Jean for the first time. This breaks continuity in two ways; first, Magneto and Professor X are enemies right? Second, Professor X is walking.
At the end of First Class, Magneto did part ways with Charles but they are by no means enemies yet. You also see this at the beginning of the first X-men. So, why couldn't Magneto and Professor X join up again? There is no reason, in fact it almost makes sense for their to be a forgive and be reconciled period with Professor X and Magneto. Now as far as Professor X walking, that's another matter. But I think Magneto and Professor X may still be friends at some time after First Class. But we shall see.