X-Men: The Last Stand co-scripter Simon Kinberg talked about characters that were left out of the movie he and Zak Penn wrote.
One myth that Kinberg dispelled for iF Magazine was the idea of a Sentinel-based storyline: "There never was a Sentinel script that veered away from the story we ended up with. I have no idea where the rumors came from, but it may have something to do with the Sentinel in the danger room. It also might have something to do with the fact that there was an earlier draft of X-MEN 2 that had Sentinels in it."
Regarding which X-stories informed his script: "One thing that I knew going in was that it was going to be the Dark Phoenix story since [X1 and X2 director] Bryan [Singer] had laid the groundwork for that in X2, but what we didn't know was what the other parallel stories would be. I think everyone felt that one of the strengths of the first two X-Men movies was that they had a number of parallel stories. In many ways the Phoenix story is the emotional 'A' plot of the film, but the political 'A' plot of the film became about the cure. That was actually a studio executive's idea. One of them had read Joss Whedon's gifted run [in Astonishing X-Men] with the mutant cure in it and thought that would be an interesting quandary for the characters. One thing that you'll find when you look online, is that whether fans do or don't like this movie (and the opinions are pretty wildly diverse as you can imagine), they certainly acknowledge that there is a lot of the comics represented in this movie. I won't claim credit for anything good in the movie except Zak and I are the biggest X-Men geeks that were anywhere around this film with the exception of Avi Arad. Zak and I were certainly the ones on set everyday, who were fighting really hard to shoehorn everything into the movie that we loved about the books."
How about Alan Cumming's Nightcrawler?
"I don't know if Alan backed out or whose decision that was. There was a draft of the script where Nightcrawler had a cameo but not a big part. I think the studio felt that either we should give Nightcrawler a major story since he was so well established in X2, or we would do sort of what the comics do, which is to move onto another story with a new set of characters knowing that Nightcrawler is out there in the X-Universe and can possibly return for some other X-Men movie in the future. Bryan did such an excellent job with Nightcrawler in X2 both in terms of representing his powers and giving him an emotional arc, that there wasn't much left to do with the character in X3. It also felt like he might tread a little bit on the terrain of Beast; in terms of similarities in the characters and their political standpoints in terms of dealing with their mutancy. We ended up jettisoning the character."
Also, "I think the one character we really wanted to find a way to include in the movie, and ultimately just couldn't find a way to do it, was Gambit. We wrote a cameo for him, and then really felt like it was better to save Gambit and give him a major role in a future X-Men movie, rather than give him a cameo where fans would be saying 'that's all I get of Gambit?' The plot that we chose for the story, felt like it was so good at introducing Beast and Angel, because of the department of mutant affairs and Warren Worthington the first being the creator of the cure. It all felt very right and very resonate. Finding a place for Gambit where he wasn't going to be just one of the team didn't come to us. We didn't want to introduce a fan favorite character and not be able to do him justice. There just wasn’t enough space in this movie."
Meanwhile, one of the concept artists that worked on the film posted an image of what Stacy X, the mutant prostitute, might have looked like had she been included (see below):
