Unfortunately the BS is motivated by money, as is all of college sports. There is a reason that the 'not-for-profit' NCAA is a billion Billion BILLION dollar business. And it isn't for rational thought, its by creating whatever game(s) will generate the most revenue.
Things the BS got wrong in my opinion:
Michigan, although its good for the college football landscape when they are relevant, shouldn't be in the Sugar Bowl. Money definitely motivated that, Michigan may travel better than any other college football team.
Boise St. getting jobbed, again. What do they have to do to not be considered a mid-major every season? Any school from an AQ who played their non-conference schedule (see: Big East) and finished with one loss would make the BCS.
National Championship Game is a rematch of 'The Game of the Century' aka 'Snoozefest Part I' aka 'Alabama's Quest for a Kicker' aka 'Three and Out'. LSU defeated Alabama in Tuscaloosa, then had to essentially go undefeated the remainder of the season including playing in the SEC Championship game, while Alabama benefited from losing the game.
Oklahoma State defeated five top 25 opponents, Alabama defeated 2. But the SEC is the 'most dominant' conference in the country. The media gets to hype a matchup that less than half the country wants to see, I think we all saw...........

. Oh, sorry, I fell asleep thinking about that first game.
That doesn't include West Virginia and Clemson getting bids more based on previous bowl tie-ins than current BCS structure.
At this point, they might as well return to the previous structure given that higher ranked teams in the BS are only allowed to play if they:
A. Travel well
B. Create ideal matchups
C. Bring revenue
D. Media can hype
The whole system is a joke, every year there is contoversy. I don't know what the perfect structure is, but the current one isn't correct.