The seeding hasn't been great. Too many games where there was an obvious talent disparity between the two teams, too many games between teams in the same region or who played in the regular season. And of course the whole thing where top seeds go to conference champions rests on the very faulty assumption that the conference champ of another conference is better than the 3rd/4th best teams in the SEC and B1G.
Before the playoffs actually happened, I was reasonably confident that with 12 teams in the field, no team that could plausibly win the national title would be left out. With Alabama being left out this year, I no longer have that confidence. And yes, I know Alabama lost their bowl game, Alabama typically loses the bowl game in years they miss the NCG, this was a hallmark of the Saban era.
I think the top seeds going to conference champs thing is a necessary evil, otherwise conference championship games become meaningless and teams start trying to avoid them. Conference championship games are a big moneymaker for the conferences and the playoffs have to co-exist with them for better or worse.
I think a lot of the other problems can be fixed by going to 16 teams. Add 3 more overall at-large spots (these will typically go to 3rd/4th place teams in the B1G or SEC, or in some years might go to the 3rd place ACC team) and 1 more at-large spot earmarked for a team from outside of the SEC/B1G/ACC/Big 12. Make on-campus games a reward for high seeding and therefore conference championships.
This should make things better while also being politically realistic.