As an aside, the objective of the BCS was never to set up a bowl system that pits undefeated teams versus each other or for the best teams to be matched against each other.
The objective of the BCS was to put into a championship game the consensus #1 and #2 team. That's it.
Remember before the BCS, the conference affiliations forced the conference champs to go to their respective bowls. So if the consensus #1 team was the SEC champion and the #2 team was the Pac 10 champion, they would never face each other. The SEC, ACC, Pac10, Big10, and Big12 all had bowls their champions had to play in which meant most of the time, getting the top 2 teams to face each other was very difficult.
So the BCS was born and promised putting the consensus #1 and #2 in a bowl to determine the national champion. They do that. They never promised that the consensus #1 and #2 would both be undefeated or that every team that was undefeated would get a crack at the national championship. The BCS is set up to preserve as much of the bowl system, tradition, money, pomp and circumstance and everything else that is the college bowl season is all about while at the same time getting the top 2 teams to face each other for the championship.
That this year they ended up with 1 v 2, 3 v 5, 4 v 6, and 7 v 8 shows that some years, they get it right.