There's no way that Boise State deserves to be in the title game if they go undefeated. They'd need Fresno State and Nevada to have 10 win seasons, and a few of the 2nd tier teams to be decent in the WAC (as Idaho was last year).
And I don't wanna hear that I'm hating on small conferences. I'm actually a fan of the MWC and WAC. The WAC is just WAY too weak. But if Utah or TCU (or Air Force for that matter) go undefeated, I'll be backing them the way I was TCU last year. That conference is way tougher. There's a reason Boise State is going there. If Colorado State were in the WAC, they'd go 8-4. And they're pretty average. Idaho last year was a crappy team that barely won alot of its games, and went to a bowl cuz they were in the WAC. When they played the 3 good teams in the conference, they were schooled.
In fact if TCU were to go undefeated, their resume would annihilate Boise's (like it did last year going into the Fiesta Bowl). The Mountain West, you could argue, is as good as the ACC. And it's better than the Big East undoubtedly.
In fact, I think rather than giving automatic bids to the 6 conferences, why don't we just give 6 automatic bids to the 6 highest rated conference champions, regardless of conference? That makes perfect sense to me. And to compensate in the bowl tie ins, all first choice tie ins are non-binding; they can be awarded to any conference champions. So say TCU wins the MWC and makes the BCS, the Las Vegas bowl can take the crappy ass Big East champ in its place, unless said team would prefer to go the 2nd choice Big East bowl.