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The 2004 NCAA Division I-A football season ended with several undefeated teams vying for a spot in the national title game, triggering controversy. In the 2003 season, no team finished the regular season unbeaten, and five teams finished the season with one loss. In 2004, the situation became even more complicated, as five teams went without losing, a record in the BCS era (this record was tied in 2009, when five teams also went undefeated and a sixth, Florida, lost to undefeated Alabama in the SEC title game). USC of the Pac-10, Oklahoma of the Big 12, Auburn of the SEC, Utah of the MWC, and Boise State of the WAC all finished the regular season undefeated. USC and Oklahoma started the season ranked #1 and #2, respectively, but the other three teams were handicapped by starting out of the top 15. Thus USC and OU played for the BCS National Championship, while Auburn, Utah, and Boise State had to content themselves with other bowl games.
The Orange Bowl proved a rout with USC defeating Oklahoma 55-19, which earned the Trojans their second consecutive AP title and first BCS title. This game, USC's victory over rival UCLA, and the BCS title were later vacated as part of the sanctions levied against USC as a result of an NCAA investigation. USC appealed the decision but was denied by the NCAA on May 26, 2011, and the BCS title for 2004 was officially vacated on June 6, 2011. The AP title was not vacated, as the AP does not punish teams for violations. These sanctions have been criticized by some NCAA football writers, including ESPN's Ted Miller, who wrote, "It's become an accepted fact among informed college football observers that the NCAA sanctions against USC were a travesty of justice, and the NCAA's refusal to revisit that travesty are a massive act of cowardice on the part of the organization."
As with previous seasons, fans of successful teams left out of the BCS were disappointed. Auburn, Utah, and Boise State all went unbeaten but were not offered a chance to compete for the championship. Auburn was especially the focus of national media attention on this topic; many thought that since Auburn managed to go undefeated in the traditionally tough SEC, they deserved a shot at the title. Adding to the BCS frustration was the fact that Auburn and Utah, though both in BCS bowl games, would not be able to play each other as a match-up of highly ranked unbeatens. The fact that the dismay over the shutout of several deserving unbeaten teams was paired with an understanding of the 2004 season details—that USC and Oklahoma deserved their top 2 BCS spots by having perfect seasons after their initial top rankings, that Auburn was fairly ranked in the preseason as a good but not great-looking team, and that Utah and Boise State played in mid-major conferences—made 2004 a seminal year for serious momentum building behind a multi-team playoff system in college football.
There was also a controversy in selecting the BCS bowls' second at-large team (Utah being the first). The University of California expected to get the invite, being ranked fourth in the BCS entering the last week of the regular season; the Texas Longhorns, who had been left out of the BCS the year before, was fifth before the final BCS rankings were released. Both teams finished at 10-1, but the Longhorns ultimately received enough support from poll voters to move into the fourth slot, which ensured they would also receive the final at-large bid. Texas coach Mack Brown was criticized for publicly politicking voters to put Texas ahead of California; Cal coach Jeff Tedford called for coaches' votes to be made public. Texas went on to defeat Michigan in the Rose Bowl, while California lost to Texas Tech in the Holiday Bowl.
The Associated Press, as a result of two consecutive seasons of BCS controversy, prohibited the BCS from using their poll as part of its ranking formula. The AP poll was replaced by the Harris Interactive poll, and the AP continues to award its own national championship trophy.
Officials are allowed to announce the number of a player committing a penalty, similar to the NFL.
Modifying the rule regarding offensive substitutions made and rushing to snap the ball before the defense can make their changes; eliminating the five yard penalty for the first offense (but stopping play and warning the offensive team), but maintaining the 15 yard unsportsmanlike conduct penalty for further violations.
Allowing the head coach to request a time-out.
Allowing the receiving team the option to enforce encroachment penalties on punts/kickoffs either from the end of the return or from the previous line of scrimmage, requiring a re-kick.
Leaping on PAT/Field Goal attempts is prohibited.
Defensive pass interference will not be called when a kicker throws a ball high and downfield to simulate a pass.
Roughing the passer will not be called if a defensive player is blocked into the passer.
In conference moves, Miami (FL) and Virginia Tech left the Big East to join the ACC, giving the ACC 11 members. Connecticut left the Independent ranks to join the Big East. Troy also left their Independent status behind and joined the Sun Belt Conference. Florida Atlantic University and Florida International University made moves up from Division I-AA and became a I-A Independents.