Why not bring in some Reverse Engineering skills that add new parts and a new skill tree to go down for crafting?
Make it where the better your reverse engineering skill combined with the more rare the item the better the chance to get a rare crafting item needed to craft a possible new (insert cool name) set item for your ship. This would give some of the blues and greens a new use and give crafting a little more depth perhaps. This could also be another means to get some of the lower tier resources for crafting as well (like the reds).
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