After playing through the game and reading all of this, I do have to say that this is all very impressive and that the story is not too dissimilar to Aliens or the prequel Prometheus, both of which have pretty amazing stories. It's amazing how many stories actually have an apocalyptic atmosphere about them, but in reality we tend to ignore the signs and continue to destroy what resources we have regardless of how many stories are essentially underlining the future for us. Just an interesting parallel.
I think a lot of people miss the story because the story, unfortunately, is subtle to the gameplay. The story is underpinned to the looting and levelling sometimes, I find the same thing in games like Borderlands, Zelda, and Fallout.