Yep, that's the thing. As soon as they go overboard trying to find the "best" way to figure out the National Championship, it will be the end of college football as we know it.
A huge playoff system would completely overshadow the regular season. Teams outside the top 40, who couldn't make the tourney regularly, would have their programs plummet. The only thing a huge playoff does is make the elite programs that much more elite. You would basically end up with minor leauge NFL with everyone else relegated to being regular season schedule filler and glorified FCS teams.
A Plus One system will be a lot more effective than a lot people will make you believe. It forces the NC winner to play at least one top 4 team before the NC, eliminating teams that play cupcake schedules and aren't very good otherwise. It also means that more than one conference will among the top 4 teams, so LSU and Bama would have to beat Stanford and Okie State to "earn" their championship berth. That will shut up a lot of people who think their team should have had a shot because of how tough their conference is.
BCS bowl games are what make FBS college football special. Full on playoffs will kill the bowls, and the rest of college football.