If travel considerations really are something the NCAA cares about, and teams really are not seeded past the first 8 in college baseball, and creating strong inter-conference rivalries and such is recognized by the higher-ups as a good thing, then here is a humble suggestion:
Bracket Louisville against Ole Miss for a Super Regional.
For the unindoctrinated, the head coach at Louisville, Dan McDonnell, made his name as an assistant at Ole Miss. In three years at Louisville, he has won a regular season Big East title, a tournament title, and trip to the College World Series, along with three straight 40-win seasons. And, I speak only for Ivory Tower, but I am still a fan of the man.
Ole Miss and Louisville, meanwhile, look good to earn a national seed and a regional, respectively, if they can take care of business in their conference tournaments. The Rebels have a long history of performing well in the SEC Tournament, advancing to four straight finals; the Cardinals should do well in their tournament.
This would be an electric match-up with big storylines and fantastic attendance; an opportunity for Mike Bianco to "put up or shut up;" and the potential beginning of a regional inter-conference rivalry that would be interesting for both teams, so long as they retain their current skippers.
I am assured by those who know that there is some method to the madness of the NCAA - of course, that's a little like Einstein's definition of stupidity - and "storylines and drama" are not (neither should they be) the primary concern of the selection committee. However, all other things being equal, this is an opportunity to generate a great deal of excitement around these programs. This is my premature plea.