I'm with HH. How conferences determine their champion is irrelevent. Just name one by whatever means you want and move on to the tournament. You're not going to run the risk of getting a losing team in the tournament the way they do in college basketball, even with a conference championship game.
Why have a tournament for football?
I think that is the question that needs to be answered. My guess is those that push for it want there to be a clear champion, right? Do you think that is what the NCAA wants? The answer to that is no, but it is not something they want to avoid. What the NCAA wants is money, pure and simple. The more the better.
Now if you understand this, the response that is typically lobbed back is "There is more money to be had in a tournament." Which is then compared to the March Madness method used for College Basketball.
The reality is that there are many fundamental differences between basketball and football that has this comparison break down. The first and obvious difference is that there IS a clear distinction between programs. Most of this has to do with the fact that you only have 5 people playing at a time and something around 15-20 players on the team for a basketball team vs 100+ on a football team. Therefore your needs are less per school, thus more talent is dispersed to more schools, thus creating situations where a small school like Xavier (for example) can put together a team that can compete and beat a typical power like Kansas (for example). Because of this there is more reason to give the smaller schools a shot, and thus it will draw more interest. If you have games like Georgia vs Hawaii every year, you will likely see similar results to what we saw in the Sugar bowl this year. The talent level is just different.
Also IF there truly was more money to be made in having a playoff, I assure you the NCAA would be all over it. They don't really have any special allegiances to the bowls other than the fact that they are already in place, thus nothing new has to be tried (or created) to put them together. AND they (the bowls) make a ton of money for the NCAA.
I also think in some pockets of the NCAA governing body they like the controversy the lack of a definitive champion brings. That means more media coverage. And as has been noted many times before, any publicity is good publicity. Therefore they get stuff written about college football long after the season is over and huge debates rage beyond that up until the games start up again. Do you hear anything like that kind of 365 day coverage about college basketball? Maybe in some pockets of the country, but not to the scale nationally that the football programs get. And I don't think it because "football is America's #1 sport", but more because there is no real answer to these debates in the current system, so people can argue all the time over the same topic.
So I don't think the Bowls are going away for a playoff system until a time when it truly is deemed more money for the NCAA to do it. And THAT is the bottom line.