I'd keep it as materials only dropping from the aliens, while having missions automatically generated from an NPC organisation that gives bounties for various bounties being completed. "Kill X amount of workers", "Kill X amount of soldiers", "Deliver X amount of materials". Stuff like that. You still go out to hunt, you're still getting rewarded but I like my loot to make sense when it comes to PvE and Aliens just dropping cash makes no sense.
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