While playing Destiny, when I received a ship that looked super ugly, except for one part. Obviously, I scrapped it, but then I had an idea.
What if, when scrapping your ship, you could salvage specific ship parts and then combine them with the parts of other scrapped ships to create your own, unique ship. Then, you could take that ship (or any ship, really) to the Shipwright and get it resprayed to whatever colour (or combination of colours) you want. Wouldn't that be so cool?
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The ships should be your vault/armory. It would give it meaning then. The larger the ship the more guns/armor/consumables you can carry.