I don't like the conference system. In a way, what Dan is saying is correct. Each team plays 8 teams once and 7 teams twice. It isn't a conference system, but it works as a de facto conference. Formalising it into a system wouldn't change the way it functions. What would change things would be if separate ladders were introduced. But again, this doesn't alter the finals set up too much either. It would be the same as, say, dividing the finalists into (1, 4, 5, 8) and (2, 3, 6, 7); having them play off like final fours and then making the Grand Final a play off between the two. Nobody seemes to like that idea when it was proposed.
What the AFL does now, and what a conference system would do are pretty similar. You'd have the same problems with inequity ( ie, some teams get easier seasons, depending on who they play).
I remember there being some talk early on when new teams were brought in that the fixturing would follow a three year cycle, with teams playing an opponent roughly 4-5 times over that three year cycle. Once that went out the window any sense of fairness in the draw went with it. It's fine having blockbusters pencilled in twice every year, but it isn't fair. Unfortunately, money spoke louder than logic.
The draw is unfair now. The only way, to my mind, to improve it is to have as many teams play each other twice as possible. If it means having a 24 or 26 game season, at least that is fairer. not perfect, but fairer.
The other problem with conferences is that it implies that we will have 16 teams for the foreseeable future. We have them until 2006, but if we lose a couple of teams after that, the whole conference system becomes unworkable. With so much doubt about the number of teams in the AFL, the best approach is to keep all teams in the same ladder/conference/whatever. That way, adapting will be easier.
I don't even want to reopen the minor premiers/knockout finals can of worms. Suffice it to say that the major obstacle to it happening is that very few people except Dan seem to like it.