Manual building override
As a start automated building helps a lot with micro but I also noticed that even though you can manually build upgrades even if your production is automated, however the same cannot be said about unit production.
As a polish I would like to see the unit production icons still be enabled even if the production line is automated and allow us to manually override the production.
Sometimes you just need those 3 siege units and switching to manual, queuing them up and switching back to automated takes you right out of the action 
-- BadWolf