The problem here is that the entire process is subjective to a group of 13 individuals opinions. There are no clear cut guidelines of what it takes to get into the playoffs. Sure, win all of your games as a P5 and you are probably in, but lose one and you are depending upon a group of people determining your fate.
While I would be just as happy to go back to the old bowl system and just enjoy the season, ESPN and the rest of the sports media have made MNC the only thing that matters in life if you are a college football program with being selected to play in their tournament the goal of your season. Gone are the days of having goals of beat your rival, win your conference and then your bowl game. Now it is win all of your games and get to the playoffs. Anything other than that is failure.
So if we are going to play in that model, we need to set up some clear cut, non subjective criteria that everyone knows and is available to all of the teams involved. (I am excluding the G5 as until they play better schedules, they are excluding themselves).
The obvious answer is win your conference. If you can't win your conference, you don't belong in the playoffs. I have not seen anyone complain that Michigan didn't get to play in the B1G Championship game due to their loss to tOSU and being that technically, they were tied for the lead in the B1G East. No one complained because everyone knew the criteria to get to the game going in. There were clearly defined rules that determined who would represent the East and did not take a vote of 13 people in a room to decide it.
If we want a system that rewards the regular season and takes the subjectiveness out of the process, go to a 5 game tournament and be done with it. Number 1, 2 and 3 get a bye and 4 & 5 play a play in game. If you really want to make it interesting, make the play in game and the next round home games for the higher ranked teams with the championship game played at a predetermined site.
You are still going to need a way to determine the pecking order, so just go by the AP poll with the coaches poll as a tiebreaker. Sure, the tournament seeding is subjective, but at least everyone gets a shot. As for ND, they would be forced to join a conference or be left out. I have no problem either way.