Allen's stats going down isn't indicative of poor coordinating. The offense as a whole realized they shouldn't be relying so much on Allen's arm and force-feeding the ball to Diggs.
They needed to play complimentary football in order to win games, which they were not doing under Dorsey. They needed to have an identity and a toughness.
I'm hoping Allen will be more efficient and less turn-over prone, which I think he will be. They made big changes in the receiver room, adding guys who complement their new identity. We should see Allen hitting more short passes to reliable catchers and generally spreading the ball around more than usual. Regardless of Cook's personal average, the run game will be efficient and it will include Allen running because you know the offense is comfortable with that.