Couple of Ideas
I don't know if they have been mentioned before, but I think these would add a great deal to the game.
Referee crews that have a rating for how often they throw flags. Say a 1-5 scale ranging from 'very few' to 'many' or something like that. Just adds a little realism since every team of officials calls the game a little differently.
Also think a more information on injuries would be helpful. It would be nice if it would say what ratings would be effected by the injury and roughly how much. E.g. ILB John Doe, Probable 1-3 weeks with a separated shoulder. 85-95% effectiveness in strength and tackling ratings; WR James Doe, Doubtful 3-8 weeks with a high ankle sprain. 55-70% effectiveness in strength, agility, acceleration, route running. This would let you get a little more information that a real coach would be able to gather by watching the guy practice, and help you make a decision on whether or not to play him.