As a long time paradox fan, im finding it pretty wild how Vic 3 gives us complete control over our economy (even to the point of being able to change production methods and tools used by individual factories in a giant nation like Russia, as if the Tsar would be poring over blueprints of a factory in Irkutsk pondering whether or not the steam donkey is worth the investment) but, even though our leader is likely the commander in chief of the military, we're not even allowed to give basic orders to our armies or reorganise them.
My thought exactly when I realized that, to produce fruits (or some specific goods), I had to enter into the right factory to change the output parameter.
Some people complained about the military micro management in previous Vics. OK. But at least, there were fruit production, or wool, and there were artillery and some other specific stuff factories.
As you pointed out, this system becomes paranoid when it comes to big states. Do you really think I would check the fruit production at Sheffield during a first class war in asia ?