Ah, good idea about inserting Ellen Page into part two somewhere. That could help tie it in better. Maybe you could even put more scene from three earlier on in two in order to blend it better. I haven't seen any of the films for a long time, but here is an idea for transitioning from two to three. At the end of two, Jean sacrifices herself, they get all broke up about it in the jet, then there is a shot of it flying off into the distance. The next scene is in the oval office with the president, then the last scene is Charles talking with Scott and Logan about Jean. They both have a good deal of finality in them since they were intended to close up the film. I am not sure how important the last two scenes are since I have not seen them for so long. If nothing really essential is said in them, which I don't think there is, I would suggest fading out from the plan flying off into the distance to the danger room scene at the beginning of three with a "*However many* Month Later" caption. I think that transition would really work. This would also cut out the scene where Eric and Charles visit Jean as a little girl (not sure how important that really is, the last time I saw the film was during its opening week, and that has been a while), and the scene with Angel cutting his wings off. If it is possible, I might even suggest cutting out Angel's character completely, or maybe somehow moving that scene to the beginning of X2 before the Nightcrawler attack in the white house, which would again contribute to merging the two films into one. If the Jean as a young girl scene is important, than perhaps it could fit in at the beginning of X2, since even X2 is a good deal about her, it would probably fit in pretty naturally.

Oh, and as for video game cut scenes, no matter how good they look, they don't look good enough to be spliced in with film footage. I think the "this many months later" would suffice to explain Nightcrawler's absence. Or if you can just find audio from the game explaining it concisely, then maybe you could squeeze it in somewhere. But it was never like Nightcrawler joined the X-Men or decided to live at the mansion, circumstances just brought him there for a short visit. An explaination would be nice, but I am not sure it is worth resorting to video game cut scene or going through a lot of effort fix.