Let's assume the legislation passes that you can pick your own rules for determining a conference champion? If so, merge the MWC, AAC and BYU. In football, have two national divisions -- an A league and a B league -- where it is the A league champion that is the league champion competing for a BCS bowl (or whatever we're going to call it now). Some grouping like BYU, UConn, Cincy, USF, UCF, Navy, Temple, San Diego St, Boise St, Fresno St., Colorado St. and Air Force. Something like that.
In all other sports, the divide is East -- West, so basically you have an AAC conference and a MWC conference under one leadership and with pooled championships at the end of the year. In the absence of one national conference of 12 or 14 teams that won't work for any sport other than football, or the ability to have a football only conference, is that about as good as we can do at the moment?