Bah, there will never be a system that establishes conclusively the "best" college team. Part of college football is to argue controversy and insult, and insist that your team from god-knows-when was the best.
The BCS system as such is BS; much better to do away with it and go back to old-fashioned bowl games that mean even less.
A championship? That's just the road to reduced revenue and more controversy.
Besides, these bowl games in sunny parts of the country unfairly favor the wussy aerial attack and west-coast BS of SEC teams. Promise me the NCAA national championship will be decided new years day on the frozen tundra of Lambeau Field, and you've got a deal.