I have heard rumors that Magneto is involved with the Magic bullet theory with Kennedy which I think would be interesting. Aside from that I think this is what should also happen in the film.
Charles is getting new students and teaching them their powers. This new Class should include Rusty Collins, Skids, Psylocke, Rictor, and Ice Man.
Havoc and Beast have become something of a student mentors.
Seeing that this is taking place during the late 60's I think Viet Nam I think Banshee should be drafted and fight for his country. There he meets Moira who has become a doctor for the soldiers. He also meets Karma.
During one of the missions he encounters a serial killer Arkady. The two fight but are caught by a new threat. They are captured and brought into a blood sport arena lead by Mojo Admas. It is there Banshee learns that Arkady is a mutant with a healing factor and death spores. The two escape leading for Mojo to learn that mutants exist and sends his associates the Reavers to go search for mutants to use in his blood sport fights with mutants as the fights while they also go on a killing spree to lead them out.
Meanwhile Charles learns that Magneto is building up an army of mutants. It is at this point Magneto wants the Us government to give him his own country or he will send a mutant on his army to attack a major city. But the Us army has plans with ex-Hellfire club member Donald Pierce who is building the Sentinels. So with Mutant blood sports, killer robots, and Magneto getting stronger by the minute, Prof. X needs a hand. In this case he needs a field leader. This leads him to discover Scott Summers. How will Alex feel of a new student sharing leadership but also finding out more then he can handle?
Prof. X, Cyclops, Havok, Banshee, Skids, Rictor, Rusty Collins, Psylocke, Ice Man, Beast.
Magneto, Mystique, Unus, Karl Lycos, Slither, Mastermind, Lorelei, Angel, Fever Pitch.
Mojo, Spiral, Longshot, Bone Breaker, Pretty Boy, Donald Pierce, Skullbuster, Arkady Rossovich, Trask, Moira
But I think a lot of time should be put into the film. Like Two Towers.