I don't think you can make any conclusions about the CFP working or not after only one year of the 12 team format.
How many years did it take for 16 seed to beat a 1 seed in March Madness? And now we've seen it twice.

I'm conflicted about the conference champs getting the bye. I want conference games to mean something and I especially want to reward the conference champions. Unfortunately this was not a good year to help justify that argument so it might go away already. I think overall I would rather err on the side of rewarding those who proved it on the field by winning the games they played than giving the committee more power to choose seeding.

I think there was too much time between the end of the regular season and the beginning of the CFP though. Some teams had a full month off. That's too much and possibly contributed to the lopsided scores we've seen.