In Prometheus, the reasons why the Engineer made us, why they created the Xenomorph and why they wanted to destroy the human race on Earth are interesting to speculate about, but they don't escape the confines of the narrative. They have not become intrinsically significant, and I think that is due to the carelessness of the storytelling and insignificance of the characters' actions.
Oh I disagree. The discussions I've had about Prometheus have been about Space Jesus's, Death Gods, Death cults, Androids, Free Will, Creation, Sex as an escape from death, Fratricide, Deicide.
Inception is a bad comparison because most of the discussions about Inception are about figuring out the plot. They're not thematic symbology debates.