The worst part is it is likely beyond repair realistically unless the NCAA goes without football for a couple seasons to brainstorm how to fix this mess, and that won't happen due to the revenue the sport brings in to the universities (and NFL).
However, I have a proposition. There are currently 130 division-1 teams and that could be reduced to 100. Have 5 conferences of 20 teams (10 in each division), with the winner of each division going to a bowl game + 1 wild card team in each conference for a total of 30 bowl games. If you are healthy and don't play in the bowl game you don't get drafted.
So...down from 125 to 100 teams, down from 10 to 5 conferences (and no more independents), and down from 44 to 30 bowl games. There is your fix for more parity, more meaningful bowl games, and a more streamlined organization