I don't think best-record-in-the-NFL should necessarily (or even usually) equate to Most Valuable Player.
Yes, the Patriots' record was impressive, but it's the offensive line that's the most valuable player on that team, not Tom Brady. Almost any quarterback could excel in that system, as Matt Cassel demonstrated. There is no quarterback in the league who has the luxury of being so casual behind the line as Tom Brady. He stands on his heels, not on the balls of his feet, and he just sort of lobs the passes downfield. Behind that line, Aaron Rodgers' statistics would be simply astronomical.
By contrast, though the Packers' regular-season record was not as good, Rodgers played a far more pivotal role in that team's success than Brady did in his. I knew that Rodgers' chances of getting the award evaporated when he left the game against the Lions, but I still think he was the most deserving candidate. Without Rodgers, the Packers are a hollow shell of themselves, Flynn's performance against the Patriots notwithstanding. Without Brady, the Patriots would still be a serviceable team.
Aaron Rodgers was far more valuable to the Packers than Tom Brady was to the Patriots.