One of the major issues I have with ship design at the moment is its lack of scope. The only real issue you have is how much stuff you can put on a hull and what stuff to put there. Where you place your weapons/defenses doesn't matter, as all weapons seem to the capacity to shoot in a 360 degree arc no matter where it's placed. I would like to eventually see a system of weapon arcs in place. Weapons pointing towards the front would only be able to fire in that direction, same with weapons pointing towards the rear, etc. The more engine power you have on your ship, the faster it will be able to turn and bring its weapons to bear. Turreted versions of weapons would require more space.
None of this currently even remotely exists in GC2's design, so these changes would definitely require major coding time to implement. However I feel this would give ship design a larger impact in the game, whereas now it's really a cosmetic issue after you've determined what exactly goes on the hull.
In a related topic, I would like to see a limitation on the number and size of extras you can put on a ship. I realize that they are primarily intended to be decorative (thus the size of 0), but if I put half-a-dozen large extras on a tiny hull, how can you justify calling that ship tiny anymore?