I think that without a doubt people have lost sight of the award from the viewpoint of what it should be. It's become something between a stats award, and a popularity contest.
The bias is abundantly clear as well, and it's one reason Alabama fans get worked up over this. Alabama has had a great history, with a lot of great players and it's astounding, especially when you consider the fact that winners usually come from top teams, that they've had only one winner, ever. Kenny Stabler, Joe Namath, Shaun Alexander, Ozzie Newsome, Derrick Thomas (all time single season college sack record, which only was enough for 10th in Heisman voting), etc...
USC, during their less dominant run, won 3 Heismans out of a 4 year stretch! Alabama has one, ever. Michigan had unorthodox winners in Charles Woodson and Desmond Howard. Alabama has one but Michigan has a cornerback and a WR both with the award? Notre Dame has 7, Ohio State has 7, Oklahoma has 5.
But, if you want to see the bias aligned against AJ, just look at some of the QBs who have won the award. Troy Smith, Jason White, Eric Crouch, Chris Weinke, Danny Wuerffel, Charlie Ward, Gino Toretta (notice any favoritism for Florida schools?), etc...
Ironically, the justification then was that if you were the best QB on what many saw as the best team, you got the award. Now, thanks to the moving target (what ever criteria doesn't include an Alabama player), it's just raw stats. There's just no way to look at that list of winners and say nah, AJ doesn't deserve it.
Troy Smith won the award with 2,500 yards passing, 6 INTs, and 30 touchdowns. I could go on listing stats, but why go farther than that? There's no question that AJ is having a Heisman worthy season.