It's sort of like when the NCAA Men's tournament expanded from 32 to 64 teams. Sure, not a lot of people liked it, but it's still the best tournament in college sports, if not all sports. To me, the super conferences for college football will be just as exciting.
So hypothetically, let's think that there's 6 conferences. Every fan of collegiate football has always wanted to see a playoff. If the top two teams come from each conference, say the winner of each the two divisions in each conference makes the playoffs, we have a 12 team like the NFL. The BCS could still come in and see the top two teams from each coast. (The East and the West will be the two sides of the bracket with three conferences on each side.) And they each get byes. Leaving us with a playoff just like the NFL.
Now, I'm not saying that this is going to happen, but it isn't such a farfetched idea if the super conferences do come to alignment. And I think it would make for a great college football season and post season.