This is a bit of a tangent, but I was thinking about the multi-mode-motors from earlier and how future strategy may revolve around the use of low-acceleration high-duration carriers fielding high-acceleration low-duration fighters.
How about the addition of a proper docking system? What I'm thinking of is that we would be able to design, say, a cruising engine module consisting of, for instance, an engine, fuel tanks, crew quarters, and engineering sections, but no bridge, active defenses, or anything else. When alone, it would be unable to function. When docked to a ship with a bridge, it becomes a fully-functional part of the ship, increasing the mass of the vessel and everything. The only thing that remains is the ability to tell the command vessel to disable the inefficient engines.
Also, it'd be nice to be able to have a way to connect ships without using tractor beams.