You bring up a good point. As I've said before, Vaughn set up the X-Men and the Brotherhood, and Singer decided against that, killing off Azazel, Angel, Riptide, Banshee, Emma Frost, and only including Havok in one scene, instead of keeping him involved.
Now, that worked fine for DOFP. But then he realized he wanted an X-Men team to fight another threat (Apocalypse), so he had to set up an extra set of characters in this movie, discarding the FC team as just a "tactical team" and calling his team the REAL X-Men to hype the movie.
And that's the problem with Singer/Kinberg "take it one movie at a time" approach. Had he kept the Brotherhood and the X-Men from FC, maybe this movie wouldn't have been so cluttered setting up so many characters. Maybe we could've even had an experienced X-Men team uniting with the Brotherhood against Apocalypse.
Or maybe they should've made a Magneto/Charles origin movie first, and then a First Class movie with the actual First Class mentioned in X1 (Jean, Cyclops and Storm) instead of retconning stuff by doing both in a single movie.
Decisions, decisions.