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I think I can summarize the arguments for a tournament in college football in two categories: 1) the current system does not necessarily identify the best team in the country and 2) the current system is anti-climatic. I'll take these on one at a time.
Does the current system identify the best team in the country? No. It's not supposed to, its supposed to identify the national champion--an ill-defined concept that breeds disagreement and debate. The reason we cannot agree on a national champion in college football is not that the BCS is flawed but that no one knows what it means to be a national champion in college football. In college basketball or college baseball or any other significant sport, the champion is the winner of a tournament. Its a definition, not a theological truth that was spawned during the creation of sport.
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If you remember nothing else, though, remember that never in college football nor at any time in any sport that I can think of is the champion the "best team". One reason is that we don't really care about the best team, but the team that has performed at the highest level. Those are different things.
But then try to define which team performed at the highest level. As the trend-o-matic demonstrates, a team's performance varies across a season. Do we find the team that has had the highest average performance, the team that has had the highest minimum, or the team that achieved the highest level at any particular time in a season? If you want a tournament, you're taking option three since the tournament can only identify the best team at the very end of the season without giving us any perspective on the team's relative performance through the season.
How often were the Giants better than the Patriots during the 2007-2008 season? Only during the Super Bowl; from September until kickoff, the Patriots were significantly better. But because the Giants had three hours during which they outperformed the Patriots, the Giants were crowned as the champions of the NFL. That, to me, is a weak definition of a champion and one that college football can avoid.
Which leads to the next issue--even if we are to place too much weight on a team's performance at the very end of the season for naming a champion, a tournament will often fail to identify which team is performing at the highest level. I discuss this more fully here, but the crux of the matter is that a team's performance, because of natural fluctuations in the players', coaches', and referees' biologies, luck, and other random events, will vary from game to game and moment to moment. Consequently, the more teams we send to the tournament, the more games teams have to win, and the less likely it is that the best team will get spit out at the end.
And any tournament in college football, in time, will expand.
2) The BCS bowl system is anti-climatic. I agree completely with that concern, but the solution is not a tournament. Ohio State had to wait almost 50 days from beating Michigan to playing LSU. I assume OSU fans stayed interested, but I had moved on to other interests (NFL, NBA, NHL, etc., there were plenty of options). Even the two weeks for the Super Bowl is too long in my opinion, but the wait for bowls in college football is ridiculous. And playing at neutral locations far from either team is a second problem (though USC and LSU have had quasi-home national championship games and that shouldn't happen either).
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But moving up bowl games is the only change I can propose. I don't want a tournament-defined national champion in college football because that will strip some of the importance of week 1 and will make college football like everyone else. I stand behind a "highest average performance" definition, but without a complete round robin so every team gets a chance to play the rest, such a definition is inherently subjective. I could write my own algorithm to identify the team with the highest average performance, but it will only be my opinion--there is no law in heaven that defines what it means to be a national champion in college football.
Addendum: If we did have a tournament, it can admit only conference champions. One very nice consequence would be that non-conference games would not affect a teams chances at winning a national championship. Consequently, teams would bulk up their non-conference schedule for the experience and cash--but remember, college basketball also started with a tournament that allowed only conference champions and now people are pushing to extend it from a field of 65 to 96. Don't play with fire.