Nick Saban basically put his foot down, and told him how to call plays, taking advantage of Milroe's powerful arm (he's a very good downfield passer) instead of forcing him to be a dink 'n dunker.
Rees had tried to make all three QB's (Milroe, Simpson, and Buchner) into copies of himself, and the results at the beginning of the year show how terrible the offense was.
Once Saban told Rees to throw downfield, suddenly, the offense got much better in all aspects. Opposing teams didn't have to simply drop 7 into short coverage every play.