Let me start off by saying that I don't necessarily believe in what I am about to say. I don't disagree either, however. It is simply something that crosses my mind from time to time when the bowl season comes around and people start their yearly clamoring for a playoff system. Basically, why is that people assume that the BCS system is wrong so often. The most common argument is that the game is played by people and the champion should be decided by people.
The logical fallacy, however, is that people are more skilled than computers to make the call of which teams are better than others. This is rather arrogant of us as humans. Granted humans are arrogant in general (heck some people even think that they are important enough that their actions have an impact on the global climate that has been around and developing for millions of years). The main problem with the BCS system isn't the fact that the MNC is decided by computers - the problem is the algorithms that are used to determine said champion.
What algorithm should be used to determine the national champion? I have no idea. There are, seemingly, infinite stastics that could be taken into account when determining a champion. Somewhere out there, though, I am sure a perfect formula does exist to determine a true national champion. Anytime a decision needs to be made, regardless of circumstance, math can be applied to aid in the decision and come out with the proper answer - football should be no different.
Until this golden formula is discovered we are stuck with lousy algorithms and biased humans. So heck, let's just have a playoff already - for now at least it has to be better than the alternatives.