How football is different than basketball: The NFL Playoffs are exclusive to the best of the best. 6 teams from each conference. It's also completely objective, it is based on record and record alone. In high school, structure varies, but generally includes just about everyone who might potentially be good enough to win a state championship. If they were to set up a tournament in college, there would be 8 maybe 16 teams. Can you imagine the shitstorm that would ensue over figuring out who the 16 best teams are and who has earned a spot in the tournament? The second and third place team of every big conference would raise hell over the fact that they could have run the table in the WAC or Conference USA and deserve the spot in the tournament over the TCUs, Boise States, and Nevadas of the world. If the system benefited those teams, then neglected small conference teams would raise hell just like they are now. It wouldn't change anything. There would still be controversy, and there would still be incessent bitching from every school that's ever won a big game over how they deserve a shot at the title/spot in the tournament. You hear some of that in basketball, but no one cares because there's 64 teams, and who really thought St. Mary's had a shot at the National Championship last year?
Why not to make BCS games the Quarter-Finals or Semi-Finals: Those games all have an incredible amount of history behind them. The NCAA isn't going to reduce them to foreplay, nor should they.
This year is very different from year's past. This isn't #1 USC getting snubbed from the National title. This isn't #4 Nebraska being in the National Championship. This isn't two-loss LSU being in the National Championship. This is a situation where the college football season produced three undefeated teams: Oregon, Auburn, and TCU. Unfortunately for TCU, the histories of Oregon and Auburn have landed them in conferences of higher profile and as such they played a harder schedule. It makes perfect sense that the National Championship be played between those two teams.