This is an intriguing idea that has been hinted at before in the context of the non-BCS schools just going ahead and arranging a complete playoff for a national championship. They start a party with a sixteen-team playoff, culminating in a national "non-BCS" championship game the Sunday after the BCS chanpionship game.
The idea is sort of like the old NFL-AFL rivalry. Eventually the media pressure forced the NFL do a game between its champion and the AFL champion, and after a few AFL victories, the leagues were finally forced to merge.
Ditto BCS and non-BCS. Then the BCS schools would be shamed into also adopting a "playoff" format to parallel the non-BCS schools.
It would require hutzpah and media cooperation, but would be great fun if it ever happened...
Unfortunately, Div 1-A rules don't allow for competition beyond the single bowl game. They would have to withdraw from the NCAA because the BCS schools will not allow a playoff.
A possibility is the "plus one" game. If the BCS does institute a 1/4 vs 2/3 mini-playoff, they will need an exception rule for that additional game. As part of a deal, the non-BCS schools could insist on hosting their own mini-playoff for their own schools.
Effectively, you would have a mini div 1A championship AND a div 1(A-) championship.
I definitely think that the non-BCS schools need to increase their visibility with their own best assets. This means putting together great matchups with the best schools they've got. The "at-large" spot could be used to invite another non-BCS, a sub-par BCS school (for target practice, or an independent.
Right now, 5 mid-major conferences are beating each other up over who will be the seventh BCS conference. Perhaps they just need to work together and increase their collective fortunes.
The Boise St vs TCU game tonight was excellent. So was the Louisville vs Miami-OH game. Mid-Majors need to keep providing these excellent matchups. If they can gaurantee them, they could probably get more TV money and hence, bigger bowl payouts.