I'm not sure if it's been brought up before, or is already planned, but...
Orders to transfer cargo, passengers, etc. to a target fleet, would be nice to have.
Some of them already exist, like troop transports can load units from another fleet for example.
But stuff like, having a lifeboat type ship, with orders to pick up lifepods, and then transfer them to another ship, that would allow some more things to be done. There is then some mechanical purpose behind designating a ship as a "Hospital Ship", to receive survivors - it'd be a ship with large passenger capacity, and boat bays for a number of fast lifeboats, the lifeboats would pick up lifepods and transfer them to the hospital ship.
Similarly, if people _really_ want to, they could then explicitly model shuttlecraft to load minerals, or passengers, from a body, and transfer them to their parent ship, rather than using the shuttle bay module. Doing that, would then give a reason for adding the command station for carrier operations to a lot more ships, which means more positions for officers, and more story potentials.