Best reason I could think of is just the sheer size of space. Say we have a fleet guarding Earth from the edge of the solar system, by edge I mean at or near th

Best reason I could think of is just the sheer size of space. Say we have a fleet guarding Earth from the edge of the solar system, by edge I mean at or near the heliopause. Consider that at that distance, it takes home base, Earth, 10 hours to relay commands to warships at the edge of the solar system. If you have one "mothership" with manned crew stationed with the automated fleet though, that crew can control an automated fleet and respond to changes in real time, making the fleet better able to respond to threats.