1. Football. The BCS will get stronger, and we may see another breakout of the colleges that play football. The big boy schools will join together in 3 or 4 superconferences and then play each other to determine a champion. The not-so-big boys, which includes Missouri, Kansas and Kansas State and a whole bunch of other schools will not be able to participate in any sort of national championship. I think you could still have these programs going on, but any hopes of a Boise State, or a Kansas or a Cincinnati playing for the national championship or in a BCS type setting are pretty much done. And smaller schools, playing on the D I level might drop a level for their football programs or create a new slightly lower level.
2. Basketball. More schools are better at basketball, and the list of "majors" is longer and I also think, easier to crack (see Butler), and the tournament in its present format allows for participation by midmajor programs, so I think the changes will be less seismic. You'll probably see more changes in the regular season.
3. Kansas City. Kansas City has long been a centering point for Big 6/8/12 hoops, both because of location and enthusiasm. Plus if KU and MU and K State all end up in different places, rivalry games might be lost or lessened, which would be a pity. So Kansas City will lose the opportunity to host championship and rivalry games, and will be a lesser participate in the national college sports scene. This will mean a loss of prestige and money. A tough pill to swallow.
Remember as you consider this: While the colleges actually do educate a few people along the way, and money is made through these big sports so that other varsity sports can go on, the primary point of big time college athletics has become MONEY. Whatever makes the most money, that is the resolution you'll see. Players and boosters may find themselves in new and uncomfortable positions.
So, buckle up, folks, cause change is coming, whether you are ready or not.