I'm going to start by saying that Boise State is a great team. They may be the #1 team. The problem with them playing for a National Championship is:
1. About 20 other teams (if not more) could accomplish the same undefeated record with their schedule.
2. What happens if Boise State does play in the National Championship game and wins. Then they come out the following year (ranked in the top 3) and run through their soft schedule again enabling them to have a chance to win another. Before you know it, they could win 5 titles in a row while only having to knock off a total of maybe 7 or 8 ranked teams in the process. That is 7-8 ranked teams in 5 years! Most teams in BCS conferences play that many in 2 seasons.
I agree that there seems to be no solution to this, however, Boise State had a chance to move to the PAC-10 and chose not to. They conveniently joined another lower tier conference while proclaiming that it was a nice step up. Really?