I think the following 3 things make for easy fixes to the biggest problems there are right now:
1. Move the transfer window to after the postseason. Could delay early enrolls by a week or two, but much better for competitive balance and much less distraction during the sason.
2. Expand the field to 16 teams, and include all conference champs. That expands by 4 teams, all conference champs in FBS divisions (so this year would have included Army, Marshall, Ohio and Jax State). That would make for zero arbitrary decisions on which conference champs were worthy.
3. Since there would no longer be byes, just seed the teams in order of quality, like basketball. If we go by the CFP rankings (and Massey for teams outside the top 25), that would result in a first round of 1 Oregon-16 Jax State, 2 Georgia-15 Ohio, 3 Texas-14 Marshall, 4 Penn State-13 Army, 5 Notre Dame-12 Clemson, 6 Ohio State-11 Arizona State, 7 Tennessee-10 SMU and 8 Indiana-9 Boise State