One heading in the Grantland article is "Bowls often take money over merit when making match-ups". It links to an August piece by political and athletic oddsmaker Nate Silver, who shows that part of the reason for such an opaque system is that vested economic interests want their bowls to host teams whose fans buy tickets and T-shirts, even if those teams suck. There are plenty of objective figures to consider. BCS stupidity exposed here; BCS hijinx here.
[Added later: I spent way too much time making scatterplots out of BCS data compared against the annual undergrad college rankings from U.S. News during the 2006-2010 period. Guess what? There is zero relationship, either with the rankings, the academic scoring system, or the trends over time; that is to say, football doesn't help or hurt the academic rankings, but still, it seems kind of strange that an athletic team gets to use the brand of an academic institution that they seem to have zero influence on.]
Of course the Onion is not to be left out of the fun either:; this is just fantastic.