I have a few ideas for ships, and would make them if i had any idea how, but i don't. One is a sort of supercarrier with a bunch of slots for cargo. This supercarrier would be the supply depot for a fleet. it would come with a herd of other freighters which would attach cargo containers to this ship and form a supply line to and from it. This ship would eliminate the need for many supply depots and could be put into a mission as something to protect.
My other idea came from something I was reading in another topic, forget which one. In this topic it talked about a large bomber, armed with a meson bomb for destroying juggernauts. I don't know if this would be possible, but you could actually show the bomb mounted to the underside as a container, but with engines, and when the bomb was fired the container would detach and fly towards the enemy ship.
Just a few ideas.