The cover athlete usually goes to a top player in the league. Someone many will consider to be the "best," and Allen is that guy. Last season alone, Allen threw for 35 touchdowns, 4,283 yards, and led his Bills to a 13-3 record. He is one of the best in the game, and looks like he can go on to have a Hall of Fame kind of career.
The only issue with this that Bills fans may have, is the fear of the "Madden curse." The Madden curse relates back to the past 20 years, after a breakout star makes the cover. What seems to have happened several times, is that this star ends up having a bad season after being on the cover. Guys like: Ray Lewis, Brett Favre, and Drew Brees are examples of this.
But, don't be too afraid of it. Many stars ended up having a great year after being on the cover, so it does not always happen. Hopefully Allen can stay healthy and have a solid year.
