Here's how I would do it:
The BCS calculations are still calculated. It may not determine the teams playing in the National Championship game any more, but its still important to keep the BCS calculation around for other purposes.
Start out with a 10-team playoff. As a concession to the current BCS system, each BCS conference will get to name one team to get an automatic bid into the second round of the playoffs.
That's six of the ten teams right there. Two of the remaining four will be champions of non BCS conferences. The two highest BCS-poll ranked non-BCS conference champion teams will get these bids.
The last two spots will be made up of the highest two BCS-poll ranked teams not already in the tournament. They can come from any conference (or be independent) and need not have won or even shared their conference title. The only other restriction will be that these two teams must have not lost more than two games during the season. Three or more loss teams cannot make the tournament without winning their conference.
In the first week of the tournament, the four teams that did not get a BCS conference bid play off according to BCS poll rank... the best poll ranked team hosting the lowest poll ranked team on their home field, and the second highest BCS poll ranked team hosting the second lowest poll ranked team on their home field.
That will reduce the field to eight teams. At the conclusion of week 1's games, the traditional BCS Bowls will select the teams to play in their game much as they do now. The Rose for example might prefer to have the Big Ten champion play the Pac Ten champion as they traditionally do.
Since a number of these matchups could be determined well ahead of the conclusion of the Week 1 games, if the BCS Bowls agree and know which team(s) they will definitely host ahead of Week 1, that can be announced ahead of time so that ticket sales and travel packages can start to be sold as is done now. But one or two Bowls won't know both or either opponent until the conclusion of Week 1.
After week two we're left with four teams. Two of the BCS Bowl sites will now host semi-final games. The BCS Bowls can determine themselves who gets to have the extra games, in all likelyhood it will rotate between sites each year.
In week four, is the National Championship game. As before, the host of the title game will rotate between the BCS Bowl sites each year.
I think this system will be great for college football. No one gets left out. Everyone deserving gets a chance. If you finish 1 or 2 in the BCS Poll, you're in. If you win your BCS Conference, you're in. Even the two best non BCS conference winners can't complain. And its all done in four weeks, and it would be a rarity that a team would have to play all four weeks. If they do, they won't be complaining about it.
