The offenses of the teams is where I see Auburn taking the advantage.
QB
Jason Campbell was the SEC player of the year in 2004, whereas Greg McElroy is considered very average even by Bama fans feelings. This is a runaway advantage for Auburn.
WR/TE
Another pretty significant advantage for Auburn here. Aromashadu, Obomanu, Taylor, and Mix were arguably the best WR core since the Spurrier Gators. Any one of those guys could break out at any time in any game for huge plays in the passing game. Although Bama had a solid core, they struggled to consistently get open and dominate at their position. Colin Peak was solid for Bama, but so to where Wallace and Bennent for the Tigers, so no true advantage there. The passing game overall for the '04 Tigers gave them a dynamic dimension that the '09 Bama team didn't have.
OL
Both teams had very good o-lines, but Bama's was much more one dimensional to the run while struggling at time with pass protection. Auburn's unit was balanced to both, and had 2 eventual 1st round draft picks on it. Slight edge to Auburn.
RB
This is the spot that is the closest to a wash on the offense. Ingram and Richardson made up a fantastic one-two punch for Bama, and along with their defense, where the reasons they went undefeated. However, Auburn had a superstar backfield of Carnell Williams and Ronnie Brown. both dominated at different times, both were seniors, and both were top 5 draft picks in the NFL. Ingram and Richardson are still a tick below them on the todem poll of great SEC backs. Edge to Auburn.
In conclusion, Auburn had zero weaknesses on their offense, not liabilities at all. Whereas, Bama's inconsistency in the passing game was a significant liability in several games. Without a weak link, it's tough to find a spot on offense that Bama's team could match up with Auburn's.