I think the second one can be seen as a mostly generic "group in a derelict/abandoned space whatever get attacked by whatever caused the ruin of the space whatever". Unless Aliens happens to be the pioneer of said generic scene and everything is a Sulaco rehash!
You're right that it has become practically a genre in itself at this point. I couldn't say if Aliens actually pioneered it, but I would argue it popularised it, even more than the original Alien did.
Even within that space though, I think story-wise Kashima is structurally very similar. It's certainly not meant as criticism, I think it's great. The side-stories like that and Kara/Saen/Anno quests etc. is some of the best stuff in the game imo.
Anyway another one I thought of for your Futurama section - Bran Flazingan (Humphard CEO) has to be a Zapp Brannigan reference, right?
I'm sure there are a ton more I'll remember on my next play through. I can't recall off the top of my head, but there must be some Hitchhiker's Guide references in there, surely?
e: if not i might have to become a writer just to get some in. i mean, given how messy it gets the tits universe might be the only one in which a towel is even more useful!