To me, Brees was not an MVP. He is a very quarterback that is on a team that throws the ball far too often. The result is huge passing yards, very nice stats, and too many losses. If this Saints team tried to control the clock and win games, running backs would be getting 25+ carries a game and passing yards would come way down, resulting in Brees looking like an above average quarterback, but not an MVP.
I can see the argument for Manning, because he made the decisions that got the team these wins. He is given the power to make the calls at the line, and most often, as long as he isn't facing a tough 3-4 defense, he gets the job done, and done well. He still isn't my vote for MVP though.
I would put Chris Johnson, Matt Forte, Adrian Peterson, Demarcus Ware, James Harrison and maybe a few more if I had time to think about it all above Manning. Given all the players I listed, if you take any of them off of their team, other than Harrison, these teams have losing records this year, IMO. I think Manning is right there close to these guys, but the fact that he is a quarterback is what giftwraps him this title for the 3rd time.