We've hashed all this out before, but the problem with 9-team divisions is that it's not really a single conference any longer. If you play a 9-game conference schedule, you literally play each team from the opposite division once every 9 years. Maybe that's okay (because 16- or 18-team conferences are stupid anyway), but it's still not a single unified conference. (The NFL gets around this with 16-team conferences by having the divisional 2-play model, a 17-game regular season, and then a conference playoff before the Super Bowl, none of which I think is palatable in CFB.)
3 divisions helps with that because you have 5 division games and 4 cross-division games each season. But then... Who goes to the CCG? Winning your division can't be an automatic CCG berth. And I think you know how I'm not a big fan of a lack of objectivity.
4 "pods" may also be a viable solution. With rotating alignment such that the four pods form annual divisions, you can ensure regular scheduling of everyone in the conference, an objective process to determine CCG eligibility, etc... But for that you need either 16 teams or 20 teams, because 18 doesn't evenly divide by 4.
Once you start having superconferences, this is just going to be a problem. Maybe superconferences aren't such a good idea...