I like Russell Wilson, but I think Robert Griffin III deserves the award. RGIII has slightly less impressive passing stats than Wilson (Wilson: 26 TDs, Griffin: 20.)
However, Griffin didn't play for a game or two this season. Despite his mid-season injury, RGIII still threw for more passing yards than Wilson did. In addition, he threw half as many interceptions as Wilson.
As for rushing, Griffin ran for 7 TDs and 815 yards, while Wilson ran for 489 yards and 4 TDs.
Griffin's stats are clearly more impressive. However, some might make the case that because Russell Wilson beat Robert Griffin in the playoffs, Wilson deserves the award. I don't think this is a fair argument because the game came down to defense more than it did quarterback play. The defense Robert Griffin had to face (Seattle) is arguably the best defense in the league. Russell Wilson had to play against the Redskin's defense. Seattle gives up 203 yards per game, while Washington gives up 380.
That's to say nothing of the fact that Griffin got hurt during the game, and actually had better passing statistics than Russell did.
Again, I like Russell Wilson, he's a shorter quarterback with a lot of talent and a lot of heart. But I just don't see the award going to him this year.