My concept for a research system is rather like Thaumcraft 3 research, but instead of Essentia, you would have certain types of technology (research areas) obtained from loot chests and sometimes pirate drops. These would include Biotech, Engines, Materials Science (hulls, glass, and so forth), Computer Systems, Weapons, Propulsion, Warp Technology, and so on. (For those not familiar with Thaumcraft 3, Essentia was basically the essence of an item; you can break that item down and use whatever types of Essentia it has for research or to create an arcane item you have already researched. The Research system basically consists of breaking a lot of items down and trying to figure out the right types of Essentia to combine. Eventually, after all of the types you need reveal themselves and you feed all of the needed items into the table, you get a finished Discovery, which can then be added to what is essentially your crafting book.)
All research areas can be researched by a character to a certain point, however after you max out all base research areas, you can choose two areas to specialize in. This would unlock special tech trees for those two areas, which would let you create rare, possibly unique (randomized) per player to a certain extent, items.
Ships would save with only standard stats (as you said), but when a ship is assembled in a Shipyard (Would replace the current ability to instantaneously "buy in" ships with the catalog), a person could put upgraded standard blocks they manufactured into the shipyard block, and they would replace the standard versions of the block in the ship that will be built. (This prevents beople from having to replace everything block-by-block, which would be painful.) Any blocks that can only be created from a recipe you obtain via special research would also need to be added into the shipyard block's inventory if they're in a blueprint.
All research areas can be researched by a character to a certain point, however after you max out all base research areas, you can choose two areas to specialize in. This would unlock special tech trees for those two areas, which would let you create rare, possibly unique (randomized) per player to a certain extent, items.
Ships would save with only standard stats (as you said), but when a ship is assembled in a Shipyard (Would replace the current ability to instantaneously "buy in" ships with the catalog), a person could put upgraded standard blocks they manufactured into the shipyard block, and they would replace the standard versions of the block in the ship that will be built. (This prevents beople from having to replace everything block-by-block, which would be painful.) Any blocks that can only be created from a recipe you obtain via special research would also need to be added into the shipyard block's inventory if they're in a blueprint.