I very much agree with the original SI article. The BCS is not perfect but it does a number of things. It gives us a champion that is closest to who was best over the entire season, not just who managed to get in and get hot at the end. It also makes the college football regular season the most intriguing in all of sports. If you don't believe that a playoff system would not impact the interest in the regular season look at the TV ratings for college BB in December and January compared to the playoffs, quick without looking tell me what are the three games today matching the highest ranked teams, can't do it off the top of your head can you. During the college football season we know every week who is playing a big game because those games MATTER. If Georgetown beats Marquette or Washington beats Arizona state or vice versa (those are two of the three games matching ranked teams) nobody outside of the schools gives a crap because all four teams will end up in the tourney and with pretty goods seeds.
If you think that a tournament gives you the best team as a champion look at the number of teams that have won the tourney with 5 or more losses on their records. A team can have a great season then end up with an injury or simply a bad match-up and the season means nothing, they are going home. If this is not enough look at the previously posted examples of teams that had mediocre seasons in the NFL who won the super bowl. Why not just be like hockey and let in half the teams playing, after all isn't that the new American way, everyone gets another chance no matter how pathetic they were when they should have been playing like a team that wanted to win.
Another question is after the tourney is over (or your playoff in the NFL, etc.) other than the winning team nobody cares. In college football we have exactly this argument running till the next season. I have no question in my mind that given a play-off Utah gets killed before they even sniff the championship game. Under the current system they and their fans can spend the next quarter century reveling in the glory of their "undefeated season", Boise can remember the big win over OU, etc.
The arguement that every other sport has a play-off is the best argument for why college football should not. It is a unique game with a unique place in American culture. It may be fun to argue about a playoff, if we had one we would argue about who should be in it. We have arguments every year about who should have gotten into the pathetically bloated NCAA BB final 65. What we cannot argue is that if we had a play-off system college football would be irreparably changed. I for one do not want screw up something that is more interesting and more fun than any other sport.