I playoff system in College Football really makes me cringe. I just don't think that the rankings are always accurate. For years, I have been a firm believer in a hierarchical points system.
Wins
Against NCAA Div I FBS = +4 points
Against NCAA Div I FCS = +3 points
Against NCAA Div II = +2 points
Against NCAA Div III = +1 point
Considering that the quality of teams declines as you go through the divisions, I do believe that the number of points you earn should also decline. Winning against Miami (OH) shouldn't earn you the same amount of points as winning against Miami U.
NCAA Div I FBS Losses
Against NCAA Div I FBS = -1 point
Against NCAA Div I FCS = -2 points
Against NCAA Div II = -3 points
Against NCAA Div III = -4 points
NCAA Div I FCA Losses
Against NCAA Div I FBS = -1 point
Against NCAA Div I FCS = -1 points
Against NCAA Div II = -2 points
Against NCAA Div III = -3 points
NCAA Div II Losses
Against NCAA Div I FBS = -0 point
Against NCAA Div I FCS = -1 points
Against NCAA Div II = -1 points
Against NCAA Div III = -2 points
NCAA Div III Losses
Against NCAA Div I FBS = -0 point
Against NCAA Div I FCS = -0 points
Against NCAA Div II = -1 points
Against NCAA Div III = -1 points
The way this would work is that FBS teams that lose against Div III teams would lose much more than if they lost against another FBS team, and that a Div III team wouldn't lose any points after a loss to a FBS team, since they are in a much lower division and that they are at a severe disadvantage.
That would guarantee that the team that beats the most best teams/doesn't lose against the worst teams would be placed at the top of the standings.