You go with a 16 team playoff (any less would be ridiculous, since there are more schools in I-A than I-AA). With there being 11 conferences, so you give 11 autobids to each conference. This ensures everyone gets their piece of the pie (even the Sunbelt gets something right now), but ultimately rewards the teams who win.
Now for the other 5 bids: an NCAA committee is put together of an equal number of members from each I-A conference (all 11 to eliminate any conference trying to bribe votes to get a second team in). They get together, break down the numbers, and come up with the 5 best non-conference winners, with the only stipulation being that no more than one at-large team can get in. They then determine the seeding, with #1 (let's say Oklahoma for argument's sake) playing #16 (Buffalo or Troy), etc, with the higher seed hosting the game in the first two rounds, and a pre-determined percentage of the revenue going to the away team.
On a side note, if strength of schedule is a factor in determining teams, it is adjusted so that ALL games are included, not just I-A games. There's no sense in punishing a school that plays a full I-A schedule and rewarding a school that plays a minnow I-AA team. This year, for example, Florida's SoS would be hurt severely for playing Citadel, as it should be. This will encourage teams to not play the I-AA schools unless absolutely necessary (ie: a team backs out on an agreement at the last minute).
You take one bye week out of the season, move the conference championship games back a week (since none of the conferences are going to want to give up that revenue) and start the playoffs in either the second or 3rd week of December, depending on whether there are 4 or 5 Saturdays in December (this year they would start the weekend of the 13th, for example), and the season would end the first weekend in January. This means teams that lose in the first two rounds would still be able to play in bowl games and have their neutral-site trip for their fans without severely hurting their attendance. The bowls would have their say in determining who they get. They could either have two playoff losers face each other, or keep conference affiliations to determine which playoff loser goes to which bowl. A playoff loss also doesn't affect bowl eligibility (say a team goes 6-6 yet wins their conference, they would still be bowl eligible).
When you get to the Semi-Finals, you introduce a 4-team playoff with a 3rd place game (functioning as a "bowl" for the 2 semi losers), in a rotating schedule with the four current BCS bowls, with each bowl getting to host either the championship or the 3rd place game every other year.
Comments? Questions? Think I've been hitting the Christmas sherry too hard? Let's hear it