Maybe there will be totally realignments based on specific sports. As it is, not all schools in conferences are competitive in all sports. As an example, Wisconsin doesn't have baseball, and Iowa doesn't have hockey. They deal with a work around, but we could actually see conferences made up of teams based on each sport, rather on a total alliance of schools as a conference.
In the end, the whole thing will be about money. It always is. Before this is through, there will be some schools who quit offering scholarship sports, because they won't be competitive, and won't make enough from their media money and game attendance to stay in business.