Any chance of getting an autoupgrade option in a future patch? Just a relatively simple thing where if you're upgrading a design, the computer will automatically equip the new design with the best of all the module types it currently has. Engines, weapons, armor, etc., will all get upgraded to the best you have available. If it goes over the space limitations, it's up to the player to fix it otherwise it won't save the design.
Alternatively, it could only upgrade within a particular series of items. Impulse Engines would automatically get upgraded to Impulse Engines III, but not to the Warp Drive series of engines. This would save huge amounts of time getting military ships updated to new technologies.
