Konami's Winning Eleven / Pro Evolution soccer has excellent AI with very few holes. For example, the players have knowledge of whether they are winning or losing and adjust accordingly. I'd be surprised if there is a single line of code in Madden that addresses this. I've never played a full season in Madden or NCAA due to the numerous AI issues but I absolutely love playing against the CPU in Winning Eleven because it replicates the real deal so accurately.
In response to the other poster, I don't think the AI problem in Madden has anything to do with processing power. The problem is just as the OP said, the AI logic is too narrowly focused on following assignments instead of understanding the bigger picture.