First off, I love the lego-sytle ship feature, and I've probably spent more so far time making designs than playing the game. It strikes me as odd, though, that my impressive and mighty-looking ships always square off against such strange-looking AI designs. What I'd love to have in DA is an invisible piece of jewelry that will act as a mounting type for the AI's autoplacement. Every time the AI places a piece, it will try to first put it on 1) a compatible mount, 2) a regular hardpoint, then 3) an incompatible mount. This way, users can customize the look of their enemies by setting size, rotation, and placement information (It would also be a great way to prevent the duplicate modules on constructors and such).
As long as the jewelry type exists in the code, it can just be modded into the game. In fact, I wouldn't mind doing this myself for the base designs.