The conference tournament automatic bid is flawed.
While the BCS takes the brunt of college sports' punches, something should be said about the pitfalls of NCAA basketball tournaments with automatic qualifiers, which is basically all of them. These teams play over 30 games just for seeding and, if they lose in the conference tournament, the whole season is for naught. It's a system that allows teams like Liberty (15-20) to be involved in the same championship tournament as Gonzaga, Indiana, and Duke.
Not every tounament has to matter and, to that point, the winners shouldn't automatically make the NCAA Tournament. Potentially, it rewards teams for having one good weekend over a four month stretch and unjustifiably ends seasons for good teams over a single bad game. Subpar mid-majors take on Goliaths and get slaughtered while more qualified teams from the same conference watch on TV.