Welcome to legislated parity. The NCAA donned their Robin Hood hat, stole from the rich and gave to the poor. Now we have a complete mess of a rankings system and annual confusion over who belongs in the MNC.
When we do finally end up in a playoff system - and you can bet your last dollar we will - they'll trace the demise of the bowl system as we know it to the 85-scholarship limit that went into full effect in 1994. We're not even four recruiting cycles away from that ruling and we've effectively neutered several of the pillars of college football, teams like Notre Dame, Michigan, Nebraska, Oklahoma, Penn State, etc, who used to be able to weather coaching storms because of the depth they built into their programs.
College football is not better off with a dominant Boise State and a weak Notre Dame. Boise State and the WAC are better off, but the sport is less healthy as a whole.