Agreed. I think the model we're heading for - which is to have two or maybe three megaconferences, each with 20-plus members, literally drawn from all over the country - simply isn't sustainable in the long run, either financially or in terms of maintaining rivalries and even fan interest. Even with increased payouts many schools simply won't be able to afford to send all of their men and women's sports teams halfway or all the way across the country to compete on a regular basis. I also think that as traditional rivalries are broken up and just a handful of teams dominate each conference in football and basketball each year (and they will) that resentment by the "have nots" will grow every year until a breaking point is reached. Add in that ESPN and Cable are a dying model and the huge payouts everyone is expecting may not be possible long-term and you've got a ticking time bomb for college sports.
I think what is probably going to happen over the next couple of decades is what you've suggested - college football will break away and form its own league, with all other sports (including basketball) likely going back to smaller, more geography-oriented conferences to save travel expenses and restore rivalries and fan interest in college sports. I don't think the idea of having 60+ college teams in just 3 conferences is going to sustainable or practical for the long haul.