I feel like lazywizard has already set the stage for this, but I would eventually like to see this mod feel less like a cheat and more like part of the game world. I feel like the "balance" could be improved if you had to provide multiple samples of a ship or weapon to allow for reproduction, alternatively destroying enemy ships in combat could occasionally drop a "design component" or blueprint that could be used instead. "If you can't buy it, fight it" type of thing. That, and of course the requirement of actual trade resources and manpower for production. Each item would have man-hours required, and a maximum number of workers to work on it. The more workers, the faster the man-hours rack up. Ability to upgrade the station over time to accommodate higher tech or larger ships.... I'm getting a little carried away now, maybe.
Then again, a lot of this will probably be added with or overruled by the eventual campaign changes.