Manipulate the environment?

i.e Transporters

Act as transporters for fleets by creating artificial wormholes

Distrupt phase lines/Phase Space for a period of time. Deter Rushers (option pick to disrupt or to create wormhole as a counter)

Trade Ship (ie possible from diplomacy tree but now at a larger scale)

Ships acting as mobile refineries for specific reserves

Models/Customization

Pick a selection of models (3 or more) for each race for a cap for ie colonizer, battleship, cruiser,frigate etc etc

Biological Warfare??