I know this is how the Oregon State Athletics Association does things... There is a championship bracket with sixteen teams, and more of the top teams are taken from stronger divisions (divisions like the one I play in, the better ones, send the top 3 or 4 teams each year, on a rotating schedule), while weaker ones get at least a team, or maybe two.
I think the BCS could be well-off for doing the same. Like, take the top three teams from the SEC, Big Ten, Big 12, the top two from ACC, Pac-10, and the top teams from Big East, C-USA, Independent, Mid-American, Mountain West, Sun Belt and WAC.
Yeah, that's more than 16... You get my point, though. They could also keep track of which conferences get more seeds than others by keeping record of interconference play.