Sins of a Solar Empire had an interesting mechanic: You could generate trade within the area you controlled, and little non-controllable trade ships would fly around randomly within the area you were generating trade. If the enemy destroyed these trade ships they would get a small amount of resources and your trade income would drop an equal amount. It simulated logistics, because an enemy army sitting in the middle of your territory disrupted a lot, but didn't add complexity to the game.

I agree, but doing so would make an interesting game. A war that's being fought by 2 evenly matched AIs, and your job is to handle the logistics on your side to give it the edge?