One more thought from the series "Flavio is going crazy".
Yesterday i was seeing an interview in which one of the producers of X1 said that in the original plot, Magneto tried to convince the X-men that they were actually being brainwashed by Charles, but they gave up the idea because the scene that showed the X-men finding out who was the real Professor would cost about 2 million dollars and envolve Jean, Iceman and more characters. But everyone remembers the lines "Are you sure you really saw what you saw?" and "This helmet will protect me from the real bad guys (X2)"
Writing yesterday to the X3 news, i remembered that Juggs and Jean joined to discover who was onslaught. So, what if Vaugn decided to bring that story to the spotlight again? (the budget now is way bigger, no money problem to do it) That would be a nice cause to introduce Juggernaut, if Professor became a kinda Onslaught (not with uniforms and all, he could just be discovered as the real villain and then go crazy and try to kill everyone). It would a very nice story, nobody would expect it to happen since Prof was always a goodie.
It may not happen, but the lines i said above are a hint that Bryan really wanted to do that, and was keeping the idea until X2, by the second line...
ahem, ok my soul is back now...