Ruuning with an idea from Orangefan (check out the BCS Banter forum):

The NCAA has mandated all I-A conferences to drop their football championship games effective with the 2008 season in favor of an NCAA-sponsored 16-team playoff after the NCAA negotiated an 11-year, $9.2 Billion TV contract with CBS.

Immediately, talk emerges about possible downsizing of 12-team conferences.

Who changes conferences, who stays?

Has little chance of going anywhere.

SEC - loses Arkansas, South Carolina, LSU
ACC - loses Georgia Tech, Virignia Tech
Conf USA - loses Marshall, East Carolina, UTEP, Houston; gains Louisiana Tech
MAC - loses Toledo, Temple (FB only), Buffalo, Miami (OH)
Big 12 - loses Texas, Texas Tech, Oklahoma, Texas A & M (reclaims Big 8 name)
MWC - loses TCU
WAC - loses Lousiana Tech; waits for Pac-10 to reduce itself by one
Big East - gains Boston College as FB only; all other sports replace Temple in A-10; talk of split gains more traction
Metro Conference (new) - South Carolina, Georgia Tech, Virgina Tech, Marshall, East Carolina, Toledo, Temple, Buffalo, Miami (OH)
Southwest Conference (new) - Arkansas, Texas, Texas Tech, Texas A&M, Oklahoma, UTEP, Houston, LSU, TCU
Sun Belt - unchanged
Pac-10 - unchanged
Notre Dame - remains indpendent

The 12 team conferences in the BCS are very influential in the NCAA. They are not going to make decisions that will eliminate parts of their respective memberships unless that is their agenda. If it was their agenda, their methodology would be per conference and not by some grand design. Power conferences could pull out of the NCAA.
There may one day be near uniformity for 12 team conferences and a sixteen team playoff. It is years away, if then. The playoff could support 12 team arrangements, rather than eliminate it, based on playoff fields being a predominance of championship game representatives. Adding one or two may be easier than shedding three or four. Twelve teams discourages the proliferation of conferences, and fewer conferences yield greater control.
1-AA has a successful model of 16 team playoff. However, 1-A is not going to let go of lucrative bowls.
Is Notre Dame still going to be an entity of "one" while everyone else must battle it out the conference route, regardless if they are a standard and uniform 8, 9, or 12?