The interesting thing about the 4x4 pods system that hasn't been brought up is that it can either incorporate a conference championship game....or not. There's no need for one. Best record (w/ tiebreakers) would be perfectly fine, with the diversity of schedules - it's more unlikely for the schedules to be that radically different, quality-wise than what we currently have in smaller conferences.
14 school conference now - play everyone in your division, play either a permanent rival + 1 rotating spot from the other division or 2 rotating spots. Either way, it's potentially unfair to play a top team from the other division every year or even the top 2 at times.
Having the play the top 2 from a pod doesn't mean as much because that's only the top 2 out of 4. All 4 may suck. A school could dominate its pod and still merely be an average team (losing the other 5-6 other conf games). Yes, the stars could align against you, and you end up playing the top team in each of the other 3 pods, but again, each of them isn't guaranteed to be a big-boy team, like the top 1-2 of a 7-team division would almost certainly be.