The NCAA should really just shut up when it comes to conference stuff.
You know who's to blame for all this realignment? The NCAA!
Two reasons:
(1) Two decades ago they enforced the 12-team/2-division model for conferences to have championship games. It was a model originally built for the D-3 level, and when the 11-member SEC asked them to waive that for D-1 the NCAA refused. So what happened? Every conference began raiding others to get to that magical, and entirely arbitrary, threshhold of 12. if the NCAA told the SEC that they can have a conference championship however they see fit, a lot of this may never have happened.
(2) Lack of an NCAA-mandated D-1A playoff. Decades of fans clamoring for a real championship decided on the field led to the Bowl Alliance, and then to the BCS. The AQ $$$ of the BCS led to this schism of have's and have nots, as well as the greed of the AQ conferences wanting 2 bids allowed (and now 3).
There's more reasons of course, but these 2 are big one's, and directly on the doorstep of the NCAA.