BCS did not work throughout the entire time it was around. It was good in getting the B1G and Pac-12 to play ball if they had number 1 or 2, but that is it.
In 2000, Miami lost @Washington to a team that would win the Rose Bowl, and beat Florida State in the regular season head to head, but the BCS gave us Oklahoma vs Florida State, and Oklahoma won 13-2.
In 2001, probably the biggest mismatch of all-time occurred. Miami played a team that couldn't even win its own division in the Big XII and gave up 50 plus points in their last game to Colorado in Nebraska. It wasn't like Nebraska didn't lose its division to an undefeated #1 team in the country like Alabama in 2011, but they got absolutely crushed by Colorado and backdoored their way to the BCS title game over a 1 loss Oregon or even a 2 loss Colorado who played a tough non-conference schedule that season and destroyed Nebraska.
In 2004, Auburn of the SEC got left out of the BCS title game for an Oklahoma-USC matchup. USC ABSOLUTELY destroyed Oklahoma. This was pre-SEC bias in the country when people were objective. USC earned their spot most felt and had actually defeated Auburn in 2002 and 2003 so they weren't questioned, but Oklahoma vs. Auburn was never really debated.
The BCS was not a success IMO, but it the job in getting all the conferences together and got rid of the B1G/Pac-12 arrogance, and it only happened because the Coaches poll gave Nebraska a split NC in 1998 after the AP gave Michigan their title. If Michigan didn't get screwed then the B1G likely would never have given away their Rose Bowl.