I'm starting to think that 12 is too many for the CFP, especially after the most recent batch of realignment that has essentially killed off the Pac 12.
I'd probably make it an 8 team field. Each "Power 4" Championship game would be part of the playoffs, and then seed the remaining 4 Champs 1-4 based on their CFP Ranking.
The G5 (or G6, depending on if the PAC survives) leagues should make their own separate playoff. I also don't care about Notre Dame's independence. I'm sure the ACC would give them some sweetheart deal, where they could still have their NBC contract and keep 100% of the money, if they joined and played a full 8 game ACC schedule. The problem is ND would have to drop a few of the lightweight schools that inflate their record every season.