I don't mind Nightcrawler's disappearance. There has never been a stable roster in the comics (only the '90s TAS, which is understandable as it is a cartoon). X-Men come and go all the time since the 1970s and return later. I don't think Nightcrawler missing needed to be explained. Besides at the hands of Rothman, Kinberg, Penn and Ratner they would have done something really stupid like cured him willingly or killed him off like they did to 90% of the characters.
Too violent makes sense for the character portrayed anyway. He could come back.
I'd personally would have liked Rogue not getting cured in X3 but coming back to join the fight at the last minute (and helping take down Magneto because there was such bad blood between her and him in X2 after what he did to her, I think Singer was building that she'd get her retribution). Then one of the last scenes would be Logan leaving to "come back one day" but driving away in Cyke's car (who I'd still want alive and shake Logan's hand after all the **** they've been through after the finale) and Rogue would be at the gate waiting, saying "Running again?" Logan would reluctantly let her in and he'd and she'd say "Heading north?" as they drive out.
It would have brought the movies full circle and hinted they'd be back. But her cured and happy and him as Cyclops with claws at the end of X3 just does NOT work.