For a couple of reasons:
1) The mid-level teams from a major conference are still better, in general, than top teams from weak conferences, their records are a result from having played much tougher opponents. (And no "doormats" qualify for bowl bids anyway.)
2) No one cares about the Boise States of the world. No one really wants to watch them, and how are you going to attract advertising and sponsorship $$$ for teams no one wants to watch?
they would watch them if they did it by playoff's.
I propose that we create a second, "lower" league then. Let's let the top 20 college teams have their own BCS league and the rest of the schools can have a playoff. The ratings can be the judge later.