The user has input on only one player at at time. He only has so much control. If you are on defense, you don't control the offense at all. Plus you don't have control over the other 10 guys on defense. If your controlling the MLB, you're not controlling your LE or any other position. The rest of your 10 players should play realistically. If your playing your MLB and the CPU is doing a pass play, your DB's should react in a realistic manner and the outcome of the play should be realistic, and the outcome of the sum of the plays in a game should be realistic.
Also,
Really the CPU should play up to a certain level. Better than a user could control someone. It should be up to the user to try and play up to that level when they take control of a player. A CPU vs CPU game should provide very accurate results. It should be the users challenge to be able to play up to how good the CPU would have performed (when the user takes control of a position).
Right now, taking control, you almost guaranteed to be able to play better than the CPU. So you have a lot of control to skew stats.