In addition to recalling 2001, the Prometheus storyline and overall vibe also strike a distinctly Lovecraftian chord, although not in the sense of implying the presence of tentacular cosmic monsters, which has become the sole connotation of the word “Lovecraftian” for many people. The film enters Lovecraft territory with its invocation of the venerable theme of ancient extraterrestrials who visited earth millions of years ago, created the human race, and left monuments and/or traces of themselves (a theme that is also, of course, central to 2001, but with a dramatically different overall point).
If you haven't done so yet, be sure to read the entire post, and also take a look at the comments section, where Cardin makes a great point that I've raised several times: namely, that using untrue or even hoax theories (like the ancient astronaut theory) in fiction isn't just acceptable but often necessary to create powerful science fiction and fantasy. The trouble comes when auteurs like Scott think their fiction embodies real-world truths and vow to use their fiction to promote false theories as a real alternative to science.
Special thanks to @wetblnkt for bringing Cardin's post to my attention.