Pretty simple, create six 10-team power conferences and a system with an 8-team playoff. The six champs get an auto bid with two at large spots awarded (independents and non power conference teams can get in this way, too).
The round robin format will produce a true champion in each conference with no unbalanced schedules. All teams will play each other once and it eliminates the guess work. There will be ties at the top from time to time, but head to head outcomes or point differentials can help break ties objectively. This takes the polls and committees out of the equation for 3/4ths of the playoff teams.
Each team will still play 3 non-conference games with the 9 conference games. This will bring better early season match ups as teams won't fear that a non-conference loss will kill their playoff chances. It will also make the conference games even more meaningful, and not diminish the value of the regular season as some argue will happen with a 8 team playoff. And without conference championship games, the first round of the playoff can be played the first week of December, and the current bowl structure with a Final Four can be maintained. This means the season isn't lengthened, thus eliminating the arguments that an 8 team playoff makes the season too long and kills the bowl system. Overall, this would probably produce huge TV ratings and more money for conferences than the current system.
Below are my proposed conferences with Notre Dame remaining an independent and Rutgers, Wake Forest, Vanderbilt, and Iowa State eliminated from the power conferences. It actually makes some pretty compelling basketball conferences, too. Have fun dissecting:
Big Ten - Michigan, Michigan State, Ohio State, Northwestern, Illinois, Indiana, Purdue, Minnesota, Wisconsin, Iowa
Pac 10 - Arizona, Arizona State, Cal, UCLA, USC, Stanford, Oregon, Oregon State, Washington, Washington State
ACC - Duke, North Carolina, NC State, Clemson, South Carolina, Florida, Florida State, Miami, Georgia, Georgia Tech
SEC - Alabama, Auburn, Tennessee, LSU, Mississippi, Mississippi State, Arkansas, Oklahoma, Oklahoma State, Texas A&M
Heartland - Texas, Texas Tech, Baylor, TCU, Kansas, Kansas State, Nebraska, Colorado, Missouri, Utah
Northeast - West Virginia, Penn State, Pitt, Boston College, Virginia Tech, Virginia, Maryland, Syracuse, Louisville, Kentucky