Should make it conference champs only allowed in
Or at lowest maybe runners up in a conference. That's a guaranteed max two teams from one conference. Say somehow a team gets to the conference championship undefeated and loses, a 12-1 team shouldn't be penalized at the last minute. Three one loss SEC teams over an undefeated FSU would be a joke.
The 4 best teams should make it regardless of conference affiliation.
For Example: Undefeated Bama beats Undefeated Auburn the last week of the season in a close game, then beats and undefeated SEC East team in the conference ship, why not allow all three teams to make it?
Of course the best four teams should make it regardless of conference affiliation. That's not the issue. The issue is that we can't truly determine who the best four teams are because there isn't enough inter-conference play to accurately rank teams from different conferences against one another.
75% of every team's schedule is conference play (8-9 games). That means 75% of the time, everyone is playing in an independent conference vacuum that doesn't contribute to inter-conference rankings. 25% of every team's schedule is out of conference games which do contribute to a baseline for inter-conference rankings, but often times those games are against meaningless opponents. Additionally, there are a lot of teams in D1 football, so the pool of inter-conference games from which we could determine inter-conference rankings gets diluted.
Short of increasing the schedule to 35 games, if they wanted more accurate NCAA rankings, and therefore a more accurate NCAA championship system, they could simply put a lower maximum on the number of conference games (5-6) and force more games against other power conference teams. But that would cost teams more money (increased travel expenses, but less of an issue now since conferences aren't really geographic anymore, travel is easier, and there is more money in college football in general) and make determining conference champions a mess because there wouldn't be enough conference play. Think about it. How often does anyone dispute a conference champion? Rarely, if ever.
At the end of the day, the schedules are set up to accurately determine conference rankings (and champions), not NCAA rankings (and champions), so media biases, conference biases, and other qualitative factors creep in to bridge the gap.