The FCS has something that the FBS does not, smaller conferences across the board (and a better way of selecting the playoff participants).
The Big Sky and MVFC plays 72.7% of their league. CAA plays just 57% of their league (CAA is going from 16 to 14 teams next year). Big South/OVC plays 100%, Ivy plays 100%, NEC 100%, Patriot 100%, Pioneer plays 80%, Southland plays 87.5%, SoCon plays 100%, UAC plays 100%
But conference size is still an issue. EVERYONE complains about the size of the CAA and their unbalanced schedule. Five teams went 6-2 in that league and among those top 5 teams each only had 1 or 2 (or none) games against the other top 5 teams.
Illinois State got into the playoffs, finished 4th in the MVFC, they did not play 2 of the top 3 teams in their league and the one team they did play, NDSU blew them the fuck out. Had Illinois State played the other two top teams in their league they likely would've went 0-3 vs them and not made the playoffs themselves.
The problem is conference size, conference size, conference size, conference size and teams not playing against everyone in their league. Solve that problem, go back to smaller conferences, eliminate conference championship games, get the top 1-2 teams from every league into a playoff and everyone is going to be much happier with how the system operates and how the process works. But it will make less money, so the schools, conferences and media partners ain't never doing it.