Perhaps have a system that restocks stores every so often, other than a command... Perhaps trade convoys?
An in-game group of ships which fly station to station, resupplying stores with basic nessecities; whilst opening up new gameplay options, such as raiding and escorting.
Along with this, we could see the implication of new ship types; transports, gunships, etc... Convoys should not be easy targets, rather, they should varry in difficulty based upon the amount of supplies their root station requires... A high tier convoy, for example, could be escorted by a gunship - a ship slightly larger than your average fighter, with alot more firepower...
On the subject of gameplay value, they would also open up an oppertunity for basic escort questing, in which a station may request the player to defend a convoy, in exchange for a random sum of credits upon its succesful arrival.