There was whining almost from Day One, and it came from Miami. In 2000, they beat Florida State head-to-head on (again!) a missed FG at the end by the Noles. And when FSU got selected by the BCS, they cried and cried, "But we beat them head to head!" Yet Miami had some selective amnesia because they always failed to mention that one-loss WASHINGTON had beaten Miami far worse than they'd beaten FSU. But they'd dismiss that with the old "but you can't use the transitive property/they lost to a 2-loss team/whatever" nonsense.
The BCS flirted with disaster in 1998, 2000, and 2001 - to the point that they had lubricated the argument once the 2003 train wreck happened. And then 2004 was almost like another train crashing into a train wreck just to make sure you knew how bad it was.
I don't think Auburn could have beaten USC that year, but it would have been a damned sight more interesting than whatever that was Oklahoma did in that game.