I wouldn't mind the hook zones issues with the stock plays so much if they at least gave us some kind of over-ride option. It looks like the issue is that the stock plays have hook zones tied to specific areas on the field. If there was at least some way to manually hot route a hook zone that would essentially just drop straight back no matter where the player lines up, then that would be a workable solution.
Realistically, they could also partially solve the problem by having the drop points tied to where the ball is, rather than to field landmarks. So for instance instead of dropping to 8-10 yards and on the hash mark in cover 3, the MLB could instead just drop 8-10 yards off the ball and about 7 yards to the left/right of where the ball is snapped from.
The problem is that right now there are literally areas on the field that are impossible to cover with zones. There is no combination of hot routes that will get a player to go and stand in the desired place. And there are actually multiple players guarding the wrong spot, so you can't even just manually take control of somebody and do it yourself, because that just leaves a hole someplace else.