One thing that still needs to be fleshed out about this MWC/CUSA championship game (aside from how the financials would work) is how each conference would determine the qualifier for the game. CUSA would still presumably have a championship game prior to the Non-AQ Bowl? If the MWC were to go to 12, then the Non-AQ Bowl Series would effectively be a 4-team playoff anyway. I'm not a huge fan of that, personally. I'd rather the MWC determine a champion in the regular season and reward the best team during the season, not run the risk of rewarding a lesser upset-minded team.
However, like you said, a 11-team MWC could have complications with ties for first place. But I'd rather have the problem of picking between two really good teams as opposed to sending a lucky inferior team ...