I was humming and harring about how to best handle 'drone' ships, but it dawned on me that a software package may be the simplest way:
Virtual Crew: While ships are vastly complicated to run, requiring highly trained crews, relatively simple operations can be performed by this software package. Virtual Crew can replace up to five pilots, gunners or sensor operators on board a ship, potentially allowing the ship to act completely autonomously if all crew can be replaced in this way. Indeed, ships can be designed without a bridge, relying purely on this software package in order to function as a drone. Ships that have no living crew make appropriate checks with a skill level equal to their Virtual Crew score, and can also be controlled through the use of the Electronics (remote ops) skill. When using Electronics (remote ops), DM-2 is applied to all checks made if the drone ship is at Long range to the controller and DM-4 if it is at Very Long range. A drone ship cannot be remotely controlled at Distant ranges and must rely on its own programming.