This is what I think plays out
Pac 16 - 10 + Colorado, T. Tech, T. A&M, Texas, Okie, and Okie State
Big Ten - 11 + Nebraska, Notre Dame, Missouri, Rutgers, and Maryland (not sure here if not them, then just swap with UConn or Syracuse)
SEC - 12 + Florida State, Miami, Louisville, West Virginia
ACC - 9 + Syracuse, Connecticut, Pittsburgh, Cincinnati, South Florida, and Memphis
Mountain West - 9 + Baylor, Kansas, Kansas State, Iowa State, Boise State, Fresno State, and Louisiana Tech
Rest of WAC merges with Sun Belt and adds Tulane for 16
CUSA has 10 teams and MAC has 13 teams with Army and Navy remaining independent (or joining CUSA to push that conf to 12).
Top 4 have automatic BCS births no problem and I suspect the Mountain West would also end up with one. The other 3 conferences would have virtually no chance at ever getting one.
Ultimately I think this leads to an 8 team playoff to decide the champion (the 4 big conferences get automatic births, the others would get an automatic if finishing inside the top
. This would not destroy bowl games as most teams would still get to go to those.