If we do get a new trilogy, I would like to see the anti-mutant histeria played out a bit more...in X1 it was slightly touched on, but when mutants become public in 'First Class' then we should see a lot anti-mutant groups/organizations arise, like Friends of Humanity, I think a good Project Wideawake/Sentinel storyline would work(look @ the success of Transformers) intro. either Gen. Lang or (the real)Bolivar Trask the Genosha arc and the start of Sen. Kelly,
From the mutant prospective, I think we should see Magneto building his Brotherhood, intro. new characters like Avalanche, and/or Toad, Sabretooth can be left out, since he has ties to Origins spin-off for now...
Mutants as side villains, I can see Sinister working, what plot IDK...Apocalypse could work, but he's mainly about the survival of the fittest and I could see him doing something like Magneto did in X1...
But I would like to Emma Frost come back as a redeeming character, either working w/Charles or starting her own school...