I posted this on the Star Ruler forums a few minutes ago, but I think it would be an Awesome idea for this game too.
Ok, what i'm thinking about is the ability to split your empire up into military zones that would be overseen by an one Admiral for each zone. These Admirals would not govern colony's...they would govern all military forces within those zones. The admirals would be able to do things like patrol the borders of your empire and in the event of war could be set to either a defensive stance or an offensive stance. That is to say that you would be able to set up a strategy for the AI Admiral and have him/her/it invade your enemy to the extent to which your strategy has dictated. You would also be able to take command personally, but you would have the option of delegating wars to your Admirals. These admirals would also be given new ships and equipment based on priority's that you are able to set....say the Orion sector is a hot bed of rebellion and discontent, so you give them more resources than say your home system sector which is secure and content...or you want to prepare for an invasion of the weakling state knows as "suckitall"...well you would increase the percentage of ships and supplies that flow to that sector until it has the resources you believe capable of waging your just war. In the event that you form an alliance with multiple Empires...something like NATO...you would then contribute to an integrated command structure and you would send a percentage of ships and supplies to the Grand Admiral of the Alliance!
"Tho' much is taken, much abides; and though we are not now that strength which in old days moved Earth and Heaven; that which we are, we are; One equal temper of heroic hearts, made weak by time and fate, but strong in will." -Tennyson