Since it is a regular season award, I still say Rodgers wins it because he had the best regular season.
Regarding Brady vs. Brees, it's close. Brees had better numbers by a little bit, but I'd argue his offensive supporting cast was much better. His offensive line didn't have the injuries New England had, and while New England's tight ends were better, Brees still had the 2nd best tight end in football with much better receivers. Brees also had Sproles and the best play caller in football. I'd still say Brees > Brady this year because they had the same record while the Saints had a much tougher schedule and Brees had better numbers, but it's close.