I just really would have liked to have seen the team growing over the course of the movies...
See the team pick up followers for the cause as they fight the good fight. Even if it could be speculated that he "never had the uniform" or what have you, I think it was made pretty clear at the end of X2 that Nightcrawler had become a part of the team. Being religious, he could have been the one to hold the memorial service for Jean (as, despite the fact that Storm would give the eulogy, there is usually a reverend or something there to "M.C." the whole thing, so to speak)
His acceptance of his mutation, despite it obviously making him an outcast, could have been a very important contrast to the likes of Rogue, who wants to take the cure. I think it's more impactful that way, than from say Storm or Wolverine, who could pass as normal humans in society, because they don't have any obvious mutations.
And it would have been an interesting arc, to see his pacifist beliefs challenged, and he has to decide between taking a stand and fighting for what he believes in, or sitting back and hoping that peace could work itself out.
I mean, sure, it sounds like a lot, but honestly, I think it could have been worked in there, and worked well within everything else we have in the film thus far. The absense of Gambit and Nightcrawler are 2 characters who I'm always going to see this movie and think "they should have been in", and despite the fact that this movie is going to be awesome, amazing, the best yet, it's always going to fall a bit short of what it could have been (in my opinion) because it didn't include a character it should have (Nightcrawler), and the character who would have made my X-Men experience complete (Gambit).