I would love to see the ability to use more than one of the ships in my inventory at the time.
It seems to me that an Admiral, maybe Vice Admiral, should be able to promote 1 or 2 of his crew to Captian & assign them command of a ship in the Admirals inventory. This way, as an Admiral, you could field multiple ships under your command.
I can see some limits being placed on this... The Admiral picks a flagship & can only field 1 or 2 supporting vessels with it. None of the supporting vessels can be of the same or higher tier.
For example: I choose a Star Cruiser as my flagship. So I would choose a Valiant Class Tactial Escort and a Discovery Class Long Ranger Science Vessel as my supporting ships.
The control would be very much like the ground or away team missions where your team follows you around, attacks threats, & uses their abilities to help you complete the mission at hand.