This is all pure speculation, but the following interesting little nugget was reported earlier in the week in the Syracuse Post-Standard, in an article concerning the rumored Big Ten expansion:
Former Syracuse A.D. Jake Crouthamel, who navigated Syracuse through the ACC expansion deal, talked to the New York Times on Monday and doesn't see Syracuse lasting in the conference that he helped form.
He predicts that Syracuse will be in a different conference in five years and that college sports will be in "utter turmoil". Jake also sees the formation of four "super conferences" (ACC, Big Ten, SEC, Pac 10) which would eventually break away from the NCAA. Emphasis is mine. Let's assume Crouthamel is correct in his predictions. I would presume the four super conferences would conduct their own National Championship tournament separate from the NCAA, basically ending the NCAA tournament as we know it. Oh, it would still exist, and would still crown the "official" NCAA champion... it would just do so without any of the power conference members.
Interesting times are certainly ahead. I think the Big Ten expansion will almost certainly destroy the Big East as a football conference. And some big name school(s) are going to get out of the bloc of power conferences (most likely Syracuse and/or Connecticut and Louisville).