I don't know if I would like that either, because we'd likely see Alabama representing the SEC most years, OSU for us, and etc. The conferences would again go with their best, rather than their most deserving.Each conference should have the responsibility to establish for themselves who their "best" team is from their conference. Even if they are unsure themselves.
Let the conferences themselves nominate one team on whatever criteria they want (including eye tests if they would like). Push this drama back into the conferences where they arise. I'm sure it'll get fixed a lot faster that way. See Big 12 adding a championship game...