The important thing is to sort out the best team. Like you said, rankings are always skewed. if you take conf champs plus teams that are ranked high to fill it out you're bound to find the best team. If you want to sort out the exact rankings of all teams through play you need to play too many games.
No system, short of the playoffs as three game series' starting in August, or some kind of round robin thing starting in June, is going to put every team in its "proper" place.
Hence why it should only be the conference champions allowed. They proved against the rest of their conference they were better. A MAC team can't complain if they can't beat an SEC team when it comes to playoffs.
A conference champ only playoff would require 4 games Total to crown the champ. Rankings need to disappear completely