Some flexibility definitely would be nice, and some BCS-like conditions have been offered up here and elsewhere for all the second and third tier bowls. The catch is how all the conferences are looking for financial certainty and how precious the New Year's Day spots have become. There is a steep dropoff in payments after those 2nd tier games, such that there is marginal cost benefit to the participants and most programs play them just for the exposure and extra practice time.
I think it truly will require a form of BCS-like conditions, wherein the pool of participants is assured $X million dollars in return for simply being allotted a spot in one of several bowls. But will the folks at the Outback and Capital One Bowls (for example) be willing to risk their position in the pecking order?
This is only necessary for teams whose leaguse choose not to equally share bowl revenue.
The Big Ten and SEC, and I think Pac Ten, pool all the bowl revenue (minus small stipend) and then dole equal parts out to everyone, so there is no real payment issue for individual teams.
Now in the Big Twelve and Big East, and I think ACC, their uneven splits (participant gets a big chunk) leave this sort of problem unaddressed. If they took care of their own houses, their members wouldn't have this problem.