While I'm sure that would show you some things, I don't think it would be the full story. I mean, how often since the start of the BCS have the bigger schools in the BCS conferences scheduled the bottom-feeders of the non-BCS conferences to beat up? It would definitely skew it a bit.
I think there could be some merit to a comparison between the conferences where both teams were ranked. Realistically the BCS bids should be based on the conferences with the "best" teams rather than on depth. I would think the majority would want to see TCU or Boise play over a mediocre team for instance and seeing how each conference has done with it's top teams against other top teams would be interesting, imo at least.