I haven't written him into my script just yet (I'm almost there), but here are my basic plans:
-Storm, Logan, Kitty, and Warren fly to Boston to stop a group of Mutant extremists named the Marauders in their attacks on weaker mutants and cure patients (the reason I'm sending these is so Bobby/Rogue/Gambit and Colossus/Illyana storylines can develop while they're gone)
-They save a mutant from and attack, and it turns out to be Nightcrawler, but it is unknown why they attacked him since he's not a weak mutant. (the Sentinels are also introduced in this scene)
-A brief outline of why he left (basically that he didn't like the violence, the official reasons that have already been given).
-Kurt's friendship with Storm re-emerges, though the main focus would be a kinship that develops with Warren. He reaches out to Warren, who is angry at God for the rejection he faces from his father and the rest of the world for being a mutant. Warren takes on the mutant name "Angel" after a comment Kurt makes about Warren's appearance.
-Then, of course, I want him to be in the final battle against the Sentinels.
Then, in X5, I'm planning to turn the cure into the Legacy Virus. Before it becomes evident that this effect from the cure is contagious, Kurt shows symptoms, and reveals that he had taken the cure during his absence. This angers Warren, as he had looked up to and admired Kurt. In a fit of anger, Warren leaves the Mansion, and ends up being tracked down by Dr. Nathaniel Essex and lured into joining the Four Horsemen, where he gets metal wings and takes on the name "Archangel".
BTW, I'd love for Alan Cumming to return as Nightcrawler; but if he doesn't want to, then I think a recast would be acceptable considering he's been gone for an entire movie now.