Currently there is 11 FBS conferences with varies number of teams.

The solution...
There should be 12 BCS conferences.
12 teams to each conference.
16 teams playoff.

The nations top 4 teams(GOLD TEAMS) get spots in the Final 8.
The remaining teams come from each of the 12 conferences.
If a conference top team is a top 4 team, the second place team enters.

First round...The lowest 8 ranked conferences play. (seeds 9 through 16)
Second round...The 4 winners play the top 4 conference representives. (seed 9/16 winners play seeds 5-8)
Third round...the winners play the Gold teams in Bowls.(seeds 5/16 winners play big 4)
4th round...winners
5th round NC

A first round team(seeds 9-16) would have to win 5 to win a NC
A second round team(seeds 5-8) would have to win 4 for a NC
A top 4 team would need to win 3 for NC.

This system allows for all FBS teams having a shot at the NC.
This system would allow a conference like the SEC to have a max of 5 teams in(unlikely but possible).
This system rewards teams up to the final regular season game.
This systems crowns the best team in the nation at the end.
A team playing a hard schedule is not punished, a team playing a weak schedule is not awarded.

I'm fairly sure it is an NCAA rule that any playoff needs to be 1/2 at-large teams. If there are going to be 12 conferences (where is this other conference going to come from?) in the tournament there would need to be 24 teams total. Probably not going to happen.

Since the Big Ten and PAC-10 are the only two conferences opposed to a playoff, I propose keeping their conference champions out of the playoff and going with an 8-team solution:

Playoff 1st round:
Cotton Bowl: #1 Big XII v. at-large
Fiesta Bowl: #1 Big East v. at-large
Sugar Bowl: #1 SEC v. at-large
Orange Bowl: #1 ACC v. at-large
(semifinal and final continue alternating between sites)

Other major bowl game:
Rose Bowl: #1 Big Ten v. #1 PAC-10

Everyone who wants a playoff has one, everyone who doesn't want one doesn't have one. This might even be better for the Big Ten: i.e. Michigan's last national title came under the old system in 1997.

My solution requires 13 additional FBS teams. There are about 13 schools looking to move up.
Maybe because it is football, the NCAA might drop that rule.

24 team playoff would more or less be consistent with the % of teams that make the mens Div 1A BB tourney (65/341) versus (24/120?). Not that I think it SHOULD or WOULD happen.

The solution to your problem is simple... let the schools run the playoff, not the NCAA, but keep the redistribution credits similar (but granted, not the same) to how the NCAA runs the basketball tournament. Run it sort of like the Maui Invitational in Basketball, except for all pratical purposes, it would be an official tournament. If I'm not mistaken, the BCS isn't NCAA sanctioned. I'm thinking having each school's profits recieved redistributed as follows:

50% goes directly to the school
30% is redistributed as among the conference as officials see fit
20% is redistributed across FBS and FCS

There, everybody gets a slice of the pie and nobody goes hungry.

As a general rule, If the NCAA is given enough monetary reasons to do so, they will make an exception to the general rules..

I had some time so I decided to visualize what your scenario may entail…
12/12/16 eh? I really think, that in this case, it’s easier said than done….
I had alot of trouble creating the 12th conference out of a depleted 1-AA....

Pacific Ten:
Colorado
Utah
Washington
Washington State
Oregon
Oregon State

Stanford
California
Southern Cal
UCLA
Arizona
Arizona State

Big Twelve:
Brigham Young
Nebraska
Missouri
Iowa State
Kansas
Kansas State

Texas
Texas A&M
Oklahoma
Oklahoma State
Texas Tech
Baylor

The Big Ten:
Rutgers
Penn State
Indiana
Purdue
Ohio State
Illinois

Michigan
Michigan State
Northwestern
Wisconsin
Iowa
Minnesota

The Big East
Connecticut
Syracuse
Pittsburgh
West Virginia
UMass
Temple

Louisville
South Florida
Cincinatti
Eastern Carolina
Memphis
Central Florida

The ACC:
Boston College
Maryland
North Carolina State
Wake Forest
Clemson
Florida State

Virginia Tech
Virginia
North Carolina
Duke
Georgia Tech
Miami (Florida)

SEC:
Tennessee
Vanderbilt
Kentucky
Florida
Georgia
South Carolina

Mississippi
Mississippi State
Louisiana State
Arkansas
Alabama
Auburn


The Mountain West
Colorado State
Wyoming
Air Force
Boise State
Fresno State
Tulsa

San Diego State
University Nevada Las Vegas
New Mexico
Texas Christian
Texas at El Paso
Houston

The WAC
Montana
Montana State
Idaho
Utah State
Eastern Washington
Portland State

Nevada
San Jose State
Sacramento State
New Mexico State
Northern Arizona
Hawaii

Conference USA
Marshall
Alabama-Birmingham
Florida International
Florida Atlantic
Troy
Georgia Southern

North Texas
Rice
Southern Methodist
Louisiana Tech
Tulane
Southern Mississippi

The Mid-American Conference
Akron
Kent State
Toledo
Miami (Ohio)
Ohio
Bowling Green

Eastern Michigan
Western Michigan
Central Michigan
SUNY-Buffalo
Ball State
Northern Illinois

The Sun Belt:
Florida A&M
South Alabama
Middle Tennessee State
Western Kentucky
Appalachian State
Georgia State

Louisiana-Monroe
Louisiana-Lafayette
Arkansas State
Texas State-San Marcos
Sam Houston State
Texas-San Antonio

The HBCU conference
Jackson State
Grambling
Southern
Alabama State
Arkansas-Pine Bluff
Prairie View A&M

NC A&T
South Carolina State
Norfolk State
North Carolina Central
Florida A&M
Delaware State