Specifically the way it all funneled the championship paths and opportunities to a handful of specific conferences (or more precisely, teams).
In the 90's, Miami and Florida State essentially needed to win 1 or at most 2 big games in cake conferences to arrive on New Year's Day unbeaten or with 1 loss and a shot at the voted title. For Miami and the Big East, that meant basically a home game against an overmatched Big 8 opponent.
The Rose Bowl collusion racket guaranteed that a legitimate contender would not be playing #1 or #2 if those teams were from the S.E.C., A.C.C., or Big 12. Hence we got split titles or teams like Penn State getting shut out altogether.
As for the B.C.S.....a computer determining which 2 teams were "the best" was the silliest thing that I ever heard. And as you mentioned, did virtually nothing to create a path to a championship opportunity for anyone outside the protected class.