Second, Lovecraft uses words like "cyclopean" and "non-Euclidean" and "primordial" to describe the Great Old Ones. In Prometheus (certainly) in the heiroglyphs left by the Engineers and in the opening montage, there is a feeling of something ancient and powerful and beyond our ability to understand going on in the worlds that are visited by the Engineers. If these aren't "cyclopean" and "non-Euclidean" I'm not sure what qualifies to fit in those descriptions.
Think about it for a moment. The Alien movies (Covenant included--which is out this May) would fit quite well with the more science-fiction bent that Lovecraft explored as it developed, probably most evident in the novella, At The Mountains of Madness, where a group of explorers in Antarctica find a lost city that holds some kind of monster (I think it was an Elder Thing).
Anyway, that's my case and I'm sticking to it. It's also (probably) why I just love everything Alien. I think I just love stories that have to do with ancient unknown civilizations from another time (similar to what you get in the background of the 1930's version of King Kong).