We will always have this weird beauty pageant invitational crap because there are too many competing businesses (conferences) that are self-serving.
If we want to play fantasy for a minute: conferences would get blown up, realigned for parity, long standing rivalries and geography as best as possible. Each division can just be the conference name instead of something boring like west/north etc
10 teams per conference, 6 conferences. Round robin, no CCG. Top 2 teams in each conference get auto bids. If needed, a wild card system can be devised.
The remaining +60 programs would be put in the new FBS-II or something with 7 conferences and 10 teams per, with their own separate playoffs. There are 136 teams in FBS, so things don't divide perfectly. Or 8 conferences in FBS and 6 in FBS-II etc.
Maybe allow some teams from FBS-II to move up (i.e. for winning FBS-II titles) and then push some of the bottom dwellers in FBS down etc based on performance.
I'm sure there are some tweaks that could make it better, but that's just off the top of my head.
--End of fantasy--