Agreed.
Let's say it's all chalk from here on out. Ohio State beats Michigan in a close game, Georgia and TCU both win out. So Georgia, Ohio State and TCU are in.
Why is Michigan eliminated for losing at Ohio State while Clemson gets a pass for losing to Notre Dame in a noncompetitive game? Michigan would have a better loss than Clemson and I'd argue Michigan's win over Penn State trumps any of Clemson's wins.
And even if we eliminate Michigan, how is there even a debate between Clemson and USC? Clemson has a terrible loss and would have one win (UNC) over a CFP Top 25 team. USC has a tough loss (on a 2-point conversion) at Utah and would have CFP Top 25 wins over Oregon State, UCLA, whoever it plays in the Pac 12 title game and, oh yeah, that Notre Dame team that throttled Clemson.
Let's say it's chalk other than LSU upsets Georgia. So Ohio State and TCU are in. USC is likely the third team in for the reasons listed above. That leaves Clemson and LSU for the final spot since we're eliminating teams that didn't win their conference.
So we either reward Clemson for running through a mediocre ACC while giving them a pass for Notre Dame. Or we give LSU two mulligans (FSU and UT). Meanwhile Georgia (arguably has the two best wins of the season) and Michigan are out.
I think the conference championship game is my biggest issue. Georgia has proven itself to be the best team in the SEC this year and is a lock for the playoff. If you made winning your conference a requirement, then Georgia has nothing to gain and everything to lose by playing that extra game (ask 2017 Auburn how it feels about that). Meanwhile, LSU gets a mulligan for Tennessee, and has nothing to lose and everything to gain.
I'd be a lot more open to a conference championship requirement if all conferences were 10 teams with a nine-game conference schedule and no championship game. But we know that's never going to happen.