It got reorganized for no reason and broke the lore. Now it will have to be retconned, when all they had to do was just keep Mysticism. There was nothing wrong with it and no reason to get rid of it, or reorganize it.
Actually I think it got reorganized for game-play reasons. They wanted 3x6 skills, 6 for each main play-style, and they wanted to bring back Enchanting for the magic branch (remember it got removed in Oblivion, but that apparently has not been mentioned here yet) now that left them with removing one magic skill, and can you honestly say there is any other magic skill with less meat on it than Mysticism ? Destruction = is like the core of most mages, restoration = never gonna go away, it′s just too important, Alteration = so popular the world would explode if it was removed, illusion is pretty important too but probably the magic skill with the least amount of meat on it after Mysticism, Conjuration = how else do they make their conjurers and necromancers pop up their daedra and undead ?
So even after the Thief got Alchemy they still had to remove one to fit in Enchanting and that particular one just had to be Mysticism.
What people should be complaining about in my opinion is the removal of skill diversity at all.