Bash the BCS all you want, but it is imperative that the BCS system handle the expansion into a playoff if there is to be one. This is something of a redundant point, as the cartel of BCS powers will not let go unless Congress tells them to. (They will hold on to their cash cow, but they will tweak the cow (a la Pablo Picasso?) to maintain the money stream.)
There are those calling for the NCAA to legally take over the I-A postseason, or for Congress to mandate it, but I believe it to be crucial to the interests of the sport that the NCAA not be allowed to get its nutty hands on the structure of college football's postseason.
So far as I see it, what is most likely to happen in the next six seasons is either a four-team, two-round system using two of the four BCS bowls plus the week-later game, OR the "plus-one" system where the top two teams after the bowls are seeded into a final game. This will solve the vast majority of of "who's in the big game" controversies and entail minimal disruption to the bowl system for teams that don't have any business playing for it all - it satisfies the most interests while disrupting the fewest.
Lest you think the wise and benevolent NCAA would do the right thing, a common-sense solution has less chance of succeeding in the NCAA than it does in the BCS boardroom. There are those who say "well the NCAA runs playoffs at other levels of football so how bad can it be?" Have you seen a lot of people at the lower division games? It's a logistical nightmare but the overall lack of interest makes up for that. (The bowl system developed before playoffs were instituted, and remained because it was profitable. The lower divisions had the NCAA fill the postseason vacuum.)
Unfortunately, NCAA control of the means that the power brokers of the game have no control. The NCAA runs the Division I-AA, II and III playoffs, and they recently expanded the D3 one to 32 teams (!). Do you think anybody coaching a top program in D3 football thought that was a good idea? Doesn't matter - the NCAA decreed and it was so.
There have also been accusations (made by NCAA flunkies) that if the NCAA doesn't run it it's not a legitimate championship. This is cheap semantics - if the top teams play and someone gets a big trophy, it's legit whether the NCAA, the BCS or the Boy Scouts of America say so.
The BCS is no worse at making the tough calls that even a four-team playoff would require. The NCAA is a capricious, double-standard-ridden, closed-source politically-correct organization. The NCAA bball tournament is run by the NCAA proper (after they bought the NIT to keep it from competing for the top teams). There is no end to the funky decisions in smoke-filled room that decided the field and draw. There's no way the BCS could be any worse at deciding who gets into a playoff.
In light of laughably lax enforcement like the Reggie Bush case
I'm not even going to discuss whether the NCAA's disciplinary oversight duties lend credibility to a postseason championship.
The biggest issue (saved for last) is the issue of money control. The NCAA decides who gets the NCAA bball tournament money, but the NCAA serves its own interests, so there's no saying what they might decide to do with the cash at the next NCAA board meeting.
The BCS is doing what it is intended to do - protect the profit centers of the game. It rewards leagues for good performance while providing coarse "revenue sharing" for conferences that are down that year. Because of the cartel nature of the system, it ensures everyone gets a say so they don't walk out of the deal. (This almost happened once, when the Pac-10 threatened to pull out in 2000 if Oregon State didn't get a BCS berth.)
Play off if we must, but keep the NCAA out of the college football postseason!