Storm using a summoned blizzard to force Jason to release his illusion's hold on Xavier makes a lot more sense if you see The Cameo of a younger Jason frozen in cryogenic stasis in Origins: Wolverine.
If you read The Once and Future King after watching the X-Men movies, you will find dozens of ways that it is relevant, some of which, based on the film commentary, the directors weren't even thinking of. For example:
Obviously, the ending of the Arthurian mythos is about good friends being divided by differing principles and priorities and fighting each other.
There's a lot of discussion (by Merlin) of the need to forget and move on from past, and even ongoing, oppression and injustice, on the basis that starting a war is inherently wrong even if you've got a lot of justification for doing so.
Arthur, early in his kingship, is described as a cheerful and idealistic young man who more or less regards suffering as non-existent due to not having truly experienced any. Now watch X-Men: First Class and look at Xavier...
It takes Professor X so much longer to find all the mutants, who are a much smaller portion of the population, then it did for him to find all the humans. The reason why had already been provided earlier in the film. Xavier had trouble locking on to Nightcrawler because he's a teleporter and his mind is slippery to a psychic. It may suggest that other mutants are mildly shielded against telepaths, and it makes sense that Professor X has a much harder time finding all of the mutants than humans who have no shielding against him.
Xavier mentions that Nightcrawler is hard to track because of his teleportation powers. With some better wording and adjustment, this could explain why Charles couldn't just command Azazel to help him at the end of First Class.
Storm is talking about Neanderthals and Cro-Magnon men. At first it seems unimportant, but then I realize it can be applied to humans and mutants: Magneto believes mutants will replace humans (theory that Cro-Magnons replaced Neanderthals), while the X-Men believe that co-existance is possible (theory that modern humans are the result of Neanderthals mating with the Cro-Magnon)
In the finale of X-Men 2, just before Storm and Nightcrawler rescue Xavier from Jason's mind-control powers, how come Storm immediately knew that the 'little girl' wasn't a little girl at all, while Nightcrawler was totally convinced? Jason was a student at Xavier's school in the past, and it's possible that Storm remembers him, and his distinctive heterochromatic eyes.
Logan tells Iceman's parents that he teaches Art. This is likely to tell a half-truth without making them concerned about their son being taught martial arts at what they believe is a regular boarding school.
Many people like to complain about how Jean's Heroic Sacrifice doesn't make any sense when it's shown she could control the jet from outside the plane. However, when looking at the full context of Jean's awakening Phoenix powers, it actually makes a lot of sense why she didn't want to risk using her powers in the jet because she in fact does not have full control of them.
At the beginning of the film in the museum, Jean suddenly starts hearing voices of everyone in the area and even starts hearing voices of characters from later in the film, while also causing the electronic equipment to go crazy until she regains control. When talking about what happened, Jean tries to dismiss it just her telepathy acting up, but Scott notes that Jean's telekintic powers are fluctuating, with her causing the objects in their room to shake whenever she has a nightmare. Jean then tells him, clearly terrified, that she feels something terrible is about to happen.
When the X-Men are trying to get away from the fighter jets, Jean manages to destroy one of the missiles targeting them but it soon becomes clear that she's once again not in control as her eyes are glowing and she's not responding to anyone, and she suddenly exits her trance just as quickly as she had entered it. Her reaction makes clear she didn't consciously realize what she was doing.
During her fight with a brainwashed Scott, she once again loses control of her powers trying to block the former's optic blast and destroys not just the room they're in, but the dam itself. The very thing that she has to save everyone from at the end of the film was something that was inadvertently caused by her. In light of all of this, it's clear why Jean decides she can't be in the plane with them as she stops the wave. She's worried she'll lose control again and end up hurting the others. This really was the only way she could save them.
