A short summary of the controversy

The argument about how to choose a college football national champion has been waged for decades.  At the highest level of college football (known as the Football Bowl Subdivision (FBS) since 2006, and Division I-A prior to that), a national champion has been named by some form of consensus since 1883.  Controversy has existed since at least 1925, when the Helms Foundation selected Alabama as the champion and the Dickinson System selected Dartmouth.  There have been split-champions at least 17 more times since 1925, most recently in 2003 when Louisiana State and Southern Cal shared the honors. 

Examples of other ambiguous championships include 1947, when the AP first selected 9-0 Notre Dame prior to the bowl season, and then reversed itself after bowl season to select 10-0 Michigan after they won the Rose Bowl (compared to Notre Dame which did not participate in bowl games at the time).  In 1975, Arizona St finished 12-0, defeating Nebraska in the Fiesta Bowl, but finished second in the national championship to 11-1 Oklahoma.  In 1977, five teams finished the bowl season with 11-1 records.  Alabama fans cried foul when their previously ranked #3 team, and easy winner of the Sugar Bowl, was leap-frogged by the regular season #5 team Notre Dame, which had handily beaten #1 Texas in the Cotton Bowl.  A similar situation occurred in 1983 when #5 Miami beat # 1 Nebraska in the Orange Bowl, jumping over #3 Auburn, which won the Sugar Bowl.  The Division I-A national championship is littered with multiple other controversies during the 20^th century.

Why does such a long history of controversy exist?  There are many contributing factors, but the primary reason is that the FBS is the only NCAA-sponsored sport without an organized tournament to determine its champion.  In 1998, after 9 consecutive years of disputes in which one conference after another felt they were cheated out of a national champion because of the existing bowl agreements, the Bowl Championship Series (BCS) was born.  The BCS was supposed to end all controversy by finally giving the top two teams an opportunity to play each other in a final game of the year.  Unfortunately for the architects of the BCS system, they did not anticipate the difficulty involved in determining which teams were the top two, so the controversy has continued.  Examples include the 2006 season, when Boise St completed the regular season 12-0 and was not invited to play the only other undefeated team Ohio St, and the 2008 season, when 12-1 Florida defeated 12-1 Oklahoma, but undefeated Utah was not deemed worthy to play either team.