I made the observation on gameday that they were essentially in 24 nickel all day long, and that since they could contain the line with only 2 linemen (albeit very athletic and strong linemen), they could deploy the rest of their personnel as they pleased.
As far as Brady being confused, I agree that he did appear to be befuddled for the most part, especially with the corners jumping the routes which you don't normally do in a cover 2 zone, IIRC.
I did read that the Arizona DC mentioned that he was already working on the gameplan for this game, as soon as the schedule came out, sometimes near the end of last season.