It might make sense for football where all the top teams would inevitably get in to the new division. Every other sport would be utterly destroyed. No more "mid-major" powers (Akron, UCSB, Tulsa) in soccer because the BCS schools are separated out, no more teams like Cinderellas in basketball; it would all be gone.
Maybe if the teams left the NCAA for just football (is that possible?) it would work. Otherwise, college athletics would be wiped out. The top schools would no longer be beholden to the rules of the NCAA, like fielding a minimum number of sports, following Title IX, or anything like that. Many of the schools would drop dozens of sports and only keep football and men's basketball.