Kirk Herbstreit made a good point today. As far as these conference championship games go, either have them across all BCS conferences, or don't have them at all.
The current system is definitely broken. The frustrating part is that it wouldn't take that much to fix it. Do six autobids from the BCS conferences, and two at-large teams based on the BCS criteria. That would give us Oklahoma, LSU, USC, Michigan, Ohio State, Florida State, Miami, and Kansas State. Bracket 'em, run a playoff within the existing bowl structure, and extend the season two weeks for the semi-finals and finals. Hell, rotate the games among seven or eight sites if needed. Fact is, we are stuck with the current system for two more years after this, and I'm not optimistic that the current system will change much after that.