In fact, the whole nature of the film is so vignette-ish that it's sometimes hard to keep track of what's happening, or why. Plot points don't flow naturally so much as happen because they have to, because without them the movie would fall apart—ironically enough, as the movie tries with its plot to argue against a deterministic universe, the way the story is told says, "Doesn't matter how it happens, so long as we get our paycheck at the end." And it's a massively disappointing move for the X-Men series to make, especially considering their place in the comic canon.
The X-Men series has always worn its allegorical nature on its sleeve. While superpowers-as-metaphors in other stories vary from the adolescent (Spider-Man) to the übermenschian (good old Superman) to the gendered (one can't help but notice the symbolism, intentional or not, behind the Invisible Woman), X-Men has always been about People Who Are Different. This is immediately obvious in the title of the school itself—"Charles Xavier's School For Gifted Youngsters" rides on the double entendre of intelligence and superpowers—but it's also clear in the way mutants have interacted with "regular people" throughout the films.
Mutants are shunned from society because of visual deformity, or because they simply can't fit in. One child named Rogue (played since the original movie by Anna Paquin) cannot physically touch anyone without slowly killing them, a power she gained during adolescence and discovered when she first kissed a boy—and, like her counterpart in Frozen, she wears perennial gloves to prevent other people from ever experiencing the "real her."
Much was made over X-2's decision to make a kid's admitting being a mutant almost indistinguishable from a "coming out of the closet" moment, but to pigeonhole the message to one specific issue robs it of its power. No matter what the context is, X-Men have always stood in for the outsiders, outcasts, the refuse and the throw-aways who feel like they've got nowhere else to go.
So the real shame of this movie is that 20th Century Fox has thrown away an opportunity to actually use this message, in favor of just making another movie whose sole purpose is getting people to see the next movie. We saw the same happen thing in The Amazing Spider-Man 2, whose tagline "His greatest battle begins" openly admitted that the movie was little more than titillation for the next installment. And when The Wolverine did the exact opposite—featured a self-contained story with character progression and no sequel hook—critics (including myself) went wild, calling it maybe the best X-Men movie to date.