Don't know whether this one was already requested, but anyway:
The main issue I have with defending my empire is the micromanagement problem that I often cannot use the game-created ship designs because they always use only "BestDefense" what is not adequate if an enemy attacks with weapons that don't match BestDefense. So I would like to see also designs with "BestArmour", "BestShield" and "BestPointDefense" so that I can choose what I like to build without always going into the ship designer, and that for every new tech level, because custom designs are not updated automatically.
At least give modders the ablility to create new blueprints with "BestArmour", "BestShield" and "BestPointDefense" if you don't want to change the game itself.