Let me first say that my affiliation and alma mater ties have no bearing in what I’m about to post. With that said…
The BCS was created to play 1 vs. 2 and the 4 bowls that were associated with the 6 large conferences at the time wanted a piece of the money pie, agreeing into that. Before the BCS, the respective games were tied (and still are outside of their year of hosting the BCS Championship) with the conferences they contracted with (Rose Bowl (Pac-10, Big 10), Fiesta Bowl (Big 12), Sugar Bowl (SEC), and Orange Bowl (Big East, ACC)). Before the BCS noone whined about their team not making these bowls when they were making almost as much money on a yearly basis. With that said, I think tying in all 4 games as the BCS instead of just the 1 vs. 2 game has clouded some fans / media as to why the other spots exist. They never existed so the best teams period go to the bowls. They existed so the bowls could still guarantee attendance with those historical conference matchups to fill their seats.
Does this mean that people have to like it? No.
Frankly, I think each conference champion should get a BCS spot. It would help fund those mid-major conferences on a yearly basis and add even more competitiveness to the already diverse collegiate football landscape. I know some of you would argue “But that would take away from the meaning of the big bowl!” Well if the only bowl that determines the national championship is the BCS 1 vs. 2, with the occasional outsider in another top bowl, then didn’t they already take away meaning from the other bowls, non Championship BCS bowls included?