The only serious problem with the Mage Tower was the choice of associated story content.

Well, that and it being part of the otherwise worst patch in Legion.

EDIT: Oh, and the fact they're removing it, and presumably all of the stories with it, just to maintain the exclusivity of the rewards - i.e. a repeat of how they stupidly handled doing so with the Legendaries in MoP and WoD - when they should keep the content in and just replace the appearances and Achievements with a handful of Gold or something.