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Really the same problem the Brotherhood's always had in the comics, its never had much of an identity outside of whoever's leading it this minute.
You had no convincing villains for the X-Men to be invested in stopping except for Pyro because of how he was Iceman and Rogue's friend before he turned genetic supremacist. Jean Grey's resurrection and the mutant cure both overcrowd the film with mcguffins and don't provide a great spark for Magneto's outright attack on the globe.
Also we never really, really get a great Magneto versus the X-Men fight. Even in X-One he mostly uses his powers to slow them down while he works his device, and 3's action is such a mess you get to see Magneto do a lot of heavy lifting but never really 'throwing a whole city worth of metal against the X-Men who desperately try to tag him hard enough to break his concentration."
Juggeranut's a waste, none of the new x-men have the charisma or energy of the lost ones, Jean makes crazy dull...in other words, a lot of it is just bad, bland direction.
