Yeah, the movies don't actually give us anything to explain it all. Basically I think Brett Ratner thought blowing him up looked cool, and Bryan Singer thought it was equally cool to forget it ever happened.
Basically--like Superman Returns pretending Richard Pryor never happened--Singer went with the fans and pretended Last Stand never happened. (Like, even if they couldn't cast a decent Forge, how did Kitty suddenly develop psychic powers??)
Oh, except to play the JJ Abrams card at the end, and say, "Well, there it is, timeline's messed up, nothing happened in the third movie, Scott & Jean didn't die after all, now can we get back to business?"
And while we're on comic-canon mistakes, will someone please explain to Singer the difference between the characters of Sunspot and Sunfire? (Sunspot was the teen student, Sunfire was the Japanese X-man who could fly and throw fire, and went on to form Big Hero 6.)
Still, the Apocalypse tease at the end felt like Lucas promising us one more Indiana Jones movie after Crystal Skull--
This one did such a good job of fixing mistakes and bringing the movie series full circle years after the trilogy had sent the very old cast went their separate ways (seriously, I don't Patrick Stewart even moved until the last scene...), you could end the franchise on this film and it would be perfect.
But no, they feel they have to put their money where their post-credit sequence is, and do one more new-cast movie. Fortunately, feels like the old non-Hugh Jackman cast has already been written off and given their gold watch in the last scene. Now maybe Jackman will finally be closer to retiring his character, like he's been wanting to do.