We should
I like the 2 team conf rule that they have in play now. The rule now is mainly there to prevent conf from hogging the BCS money, as every game outside the title game is all about money.
Even for the playoff, there are years when the SEC could have 3-4 teams in the top 12. Part of the reason for the high ranking is based off their SOS (ie conf schedule). I don't think that a conf, no matter what their rankings is, should have 1/3 or 1/4 of the available spots. A team can control their OOC games, but they can't control their conf schedule. If a B10 or SEC team loses out on a 3rd or 4th team, so be it.
Remember, that 3rd team that get cut off could have handled it on the field with the other two conf qualifiers. We have H2H to determine that where the majority of the time when we compare two teams from different confs, they didn't play.
I can see your argument, but only way I wouldn't even consider 3 teams is in a 16 team playoff. Or if another team isn't in the top 16 of the BCS (i.e no one to fill the 3rd team's slot)