Hmm... Mark Strong as Sinister? Me likey! I was thinking Jason Isaacs or Jonathan Rhys-Meyer but I like the sound of Strong as Sinister.
Of course I am totally pushing for Ewan McGregor to portray a young Magneto. Daniel Craig wouldn't be so bad either but Ewan to me looks like he could be a young Ian McKellan.
I guess if I were to go for an antagonist or antagonists in this I would say the Hellfire Club or Sinister and his henchmen. Magneto and Xavier could be running the Academy together alongside Hank McCoy, but when mutants are starting to be found out or come out to the public, the public at first takes a nasty tone towards them, and some humans and mutants are killed. This of course would bring up Xavier and Lensher's differing views on what to do--- Magneto would seek retaliation and revenge while Xavier would seek a more direct and diplomatic approach. A young Toad, Avalanche, and Mystique could take sides with Magneto and disband. Sabretooth could cameo. Xavier though believes Sinister is stronger than both him and his students and Magneto and his kids.
Magneto and his kids get captured, Xavier dispatches his X-Men to save Magneto's hide, and together, like X2 they team up, but it becomes more of a war; bickering sides turning on each other while the same time trying to stop Sinister. Sinister lives, but a few of Magneto's kids he's taken under his wing die, thus why Toad and Mystique and Sabretooth are the only remaining heavies he has left.
Sinister, having the powers he has, would live on, and promise to return---setting up a future sequel with him working with Apocalypse.