My requirements for fleet controls are pretty damned simple, really.
1. "Stay with Mothership". Designate the ship I control as the mothership. All AI ships will try to stay within X distance of me.
2. "Return to Dock". My mothership will also be a carrier. I want to be able to hit a button and tell every ship in the fleet to come dock to me so I can make a jump/recover drones/etc.
After we have those, then I can start wanting stuff like programmable patrol routes, automated factories manufacturing goods with automated cargo ships hauling said goods to a shop to sell for a steady income of credits, etc.
But for now, I'd be quite happy with "Actually have the fleet follow me around" and "God I never want to make another disposable drone rack for as long as I live!".