If you look at the history of the major sports leagues in America, you will notice that each of them came to prominence not by the labors of the players, or the owners, but by a strong commissioner. Great players and savvy owners help, but they will never put a league over the top by themselves. Major League Baseball came into prominence after Kenesaw Mountain Landis stabilized the leagues with an iron fist. Most people give credit to Pete Rozelle with giving the NFL the promised land, but in truth, he was only playing Joshua to Bert Bell's Moses. The NBA was faltering until the steady hand of Larry O'Brien cleaned up shop. Strong commissioners build strong leagues.
As it stands, the NCAA sets up discretionary rules, but the day to day running of the monster that is college football rests in the universities. Each one has its own standards, and looks out for its own interests. This dispersion of authority makes it difficult for broad changes to take place.
In the place of this system, a commissioner of college football needs to be appointed. He should have the power to rule on sanctionable offenses, eligibility issues, funding, and crowning a champion. The commissioner will be empowered to set up deputy commissioners who will oversee the individual cases in each subject.
The Commissioner should be someone with a solid background in mediation. This is evidenced by Landis being a judge, and O'Brien being a cabinet member under LBJ. A footing in business and sports law would be good, but isn't required as much a strong personality. The first name that sprang to mind was Nebraska AD and former congressman, Tom Osbourne. Then another important criterea came up, impartiality. While I would feel confident that Osbourne would be a solid commissioner, I can think of some Oklahoma fans who would be crying foul the whole time. As I looked through the list of former commissioners, most didn't attend an FBS College, and worked through the league office, rather than with a specific team. This allowed for objectivity, which is a must in this situation, not only from the commissioner, but towards the commissioner.
With a strong central authority consolidating power, it will smooth the transitions that college football will go through as it becomes a fair and competitive league.