This is going to continue to be a problem for College Football. With 12 teams getting in, and likely more in the future, this is going to lead to more debate, not less. More teams are going to feel snubbed, no matter how they work out the selections, straight record, strength of schedule, viewer ratings, etc. I will say that these teams that are in the mix for say the 8-12 spots, they are probably not going to win the title. They could win one fluke game, but not likely they win 3 games.
Teams are still going to gripe if they finish 13th or 14th and don't get in. But when you had 4 teams, the 5th and 6th teams that didn't get in had a better chance to win the title. So yeah, some teams/fans are going to gripe, but if you are 9-3 or whatever, it is hard to make an argument that you have a legit chance at the title.