[CMIII]

ok so heres what has changed:

X-Men (1999) Mystique was not with the Brotherhood of Mutants so it's possible that Senator Kelly and his aid are still alive. Rogue does have the white hair streak so the battle of the Statue of Liberty still happened just without Mystique.

X-Men 2: With Mystique not in the picture Magneto would likely still be in the Prison from X-Men with a Limited chance of escape. While Yes Stryker would have gone to the X Mansion it's Likely that Jeans Powers never would have gone nuts. Magneto would not have been a Alkali Lake and there for the death of Jean Grey would never have happened. Also Pyro never would have gone with the Brotherhood.

X-Men 3: All event are highly Unlikely since Magneto would still be in Prison. Jean would not have become Phoenix having not died in X-Men 2. This means Scott and Professor Xavier never would have died, neither would have Jean. Also Rogue may never have gone for the cure, Neither Magneto or Mystique would have been cured. Also Calypso would still be alive.

Wolverine: Much like X-Men 3 most events are Unlikely to have happened at all