You made a point above. The BCS criteria is driving much of this and the new BE football will be, at best , on the fence if a similar BCS criteria continues.
It would be difficult to say, a year or two down the road, who among the BE, WAC, C-USA, MWC, or MAC would be most deserving. The lines between them could get real slim. I expect each of them will have one to three schools each year with excellent records. Each will have dormats. Teams such as TCU, Marshall, Fresno
State, Boise State, Utah, Colorado State, Toledo, BGSU, and Northern Illinois could continue to do well. Or, they could have problems and other conference companions deserve notice.
Rather than the BCS thing creating cutthroat positioning and alliances among the left-outs, the BCS needs to revise its criteria. It hurts recruiting and renders less revenue for schools that do not have the BCS label (East Carolina-all downhill since the BCS). Essentially what the BCS has done, it created a separate, elite division.
The BCS needs to have a means of realistic access for the 1-A conferences currently left out. Whether that means adding another bowl, and/or offering two more conferences direct access, needs to be examined.
To ask, for example, if C-USA would be more deserving than the MWC, is sort of like asking which is better--the Big12 or the SEC or the Big10. It depends on who you ask, what data one chooses to use, and what year one is asking, or what sport or all sports?
The BCS currently claims that any school can be garanteed a spot if it receives a #6 ranking or higher. This is true, but it is also a more lofty criteria than simply winning the conference championship; and at large bids not only concern ranking, but fan base, tradition, and media attractiveness as well.