Remember that you're casting this vote before any of the bowl games are played. Whether or not it was "right" in hindsight doesn't matter.
I'd love to hear from readers on this. Here's Homerism's attempt:
My objective would be to determine the two teams "most deserving" of playing in the title game. In that sense, I'm not really interested in trying to figure out who would win a playoff. I'm looking for the two teams whose resumes reflect the greatest achievement during the regular season.
Winning is the name of the game. If you're a BCS conference team with an undefeated record, that's the most important thing to me. This means you brought it week in and week out. No one beat you. You've earned the right to play for the title. Schedules may vary in terms of strength, but for the most part, there isn't enough difference between them to justify excluding an unbeaten team from the game. The case would need to be very egregious for that to happen--a Bill Snyder-type schedule comes to mind.
(Obviously, the rest of these factors come into play when evaluating multiple unbeaten teams or when there are no unbeaten teams.)
Who did you beat? Who did you lose to? Also, no points for trying to schedule hard and it not working out (e.g., OU beating Washington this year). The issue is how good the opponent was when you played it. My thinking is that if you're doing your OOC scheduling the right way, playing an opponent during a downturn shouldn't really affect you. You may catch another opponent during an upswing. It balances out over time.
If a team goes on the road and beats a quality team, that says a lot, in my book. If a team loses at home, that says a lot, too.
4. "Nature" of Wins/Losses
Whether it's a W or an L is most important. However, even though I don't like getting down into the weeds like this, sometimes you have to look at the manner in which a team won or lost.
Bottom line for me: Win all your games and you should be fine.