hmm I wouldn't change much I think we, as fans, could twork what we got:
X-Men 1
Team: Prof. X-Cyclops,Jean,Gambit,Storm intro. Rogue & Wolverine
Students: Jubilee, Iceman, Pyro, Kitty
BoM: Magneto-Mystique,Toad, Sabretooth,Quicksilver
Gov.: Senator Kelly, Friends of Humanity(minor role)
Plot elements: Mutants/Humans are in a fight for dominance, FoH role is shown to the ugly side of humanity, relationship between Magneto/Pietro is explored(think W&XM cartoon) also Rogue/Gambit(just mild flirtation), add the scene(s) w/Storm and Jean that didn't make it in2 the film,Cyclops has more of a leader-role(90's cartoon), Wolverine/Sabertooth history is slighty touched on, fight on Liberty Island is more epic; Scott/Jean vs. Quicksilver
X2 nothing major, more focus on Gambit's past,relationship w/Rogue, Storm's origin, I would swap the story Iceman had & give it to Pyro since it would make a greater impact of him leavin and going to magneto's side, action squence when both teams enter the spillway, Stryker makes a reference to "team X" when he confronts logan, brigther phoenix effect
X3; Plot would focus around Genosha, + Rogue/Colossus to the team, return of Jean and explain her origin, Sentinels
X4: Cure plot, return of Magento w/Avalanche, Morlocks, Dark phoenix, intro Beast/Angel