Honestly if I had to guess the four best teams in the country today 3/4 of the playoff teams would not be among them. Alabama, Ohio State, Stanford, and either Notre Dame or TCU all look better to me than Clemson, Oklahoma, or Michigan State. Yes, this is in spite of Oklahoma beating TCU by a point at home while TCU was starting their backup as well as Michigan State beating Ohio State while never leading thanks to some questionable play calling + catching OSU napping after ten straight walkovers (that would not happen again if they were to rematch).
That being said it would sort of invalidate the season if suddenly the committee were like 'we think in a rematch OSU would've won so we will just assume they did', but it does go to show that the Football system is kind of broken. A more comprehensive tournament like NCAA Basketball has would certainly not go amiss, though there's no way they could do that since they would then be subjecting College Football players to an NFL season's worth of games on top of schoolwork (lol) etc.
I actually think the best thing to do would be to do some sort of rotating 6-8 game schedule to determine the top 32 teams, and then have those teams face off in a tournament over what would've been the last five weeks of the season. The finals can be played out during bowl season and teams which come on strong late in the year could still improve their bowl placement to play a team that lost in the 'official' tournament. It wouldn't screw anyone over but it would give teams incentive to play strong competition from the get-go and would create a lot more meaningful games throughout the year.
Of course the NCAA would never go for it since it would be spitting in the face of 'tradition' but it's fun to think about.