THE INTERNETS - Kotaku.com reports that "In testimony during the class-action lawsuit against the National Football League Players Association, over royalties owed to retired players whose likenesses were used in Madden, EA's Joel Linzer said they made the decision to put Favre on the cover before he announced his retirement. When Favre announced his retirement, they considered replacing him with an active player, then bulled ahead and kept him on the cover. He later unretired."
However, since that testimony EA has retracted that official stance and instead claimed they have not used Brett Favre on the cover of their game AT ALL, but rather, what you see is Wabrettio, Brett's evil twin. (Seen above).
It's a very clever defense, since clearly that is a different person because he has a handlebar moustache.