The X-Men has always been something of an allegory for racism and other forms of bigotry with the message being that bigotry is bad and that humans and mutants can peacefully co-exist. This movie sent a very different message to me.
The anti-bigotry message of the X-Men works because it encourages people (especially comic book fans with feelings of alienation) to identify with the mutants, to look at things from their perspective, and to see them as the undeserving targets of irrational fear and hatred. But given terrorist situations in the real world, I identified, instead, with the Secret Service agents trying futilely to save their presidident from a rampaging mutant as well as with the various humans who were menaced and were controlled like puppets, not only by the evil bad guys but by the supposed good guys, as well.
Same with identity stealing mutants. They put themselves as superior races to humans.
The whole notion of mutation in the Marvel universe is crap anyway. Persons who are "born" mutated are treated differently than those who mutate as a result of some outside influence. Also in the Marvel world, siblings sired from the same parents will have different mutant abilities than each other and even their parents. A mutation should be heriditary (possibly regressive).
It's not like there is one switch "Mutant ON/OFF" that means if you have it you will have 1 of 300,000 different abilities. Crap science. Crap politics. Don't think about it too much and tell the writers to use Western Union if they want to send messages.