I still firmly believe that Prometheus is a fascinating mess. It is terribly paced and edited (especially during the final third) and it has quite a few really stupid scenes throughout, but I can't help but love it more and more every time I watch it.
I find the themes and concepts that the film portrays to be absolutely, dare I repeat myself, fascinating. I completely understand and sympathize with those who do not like that the Lovecraftian cosmic horror that was the Space Jockey was transformed into humankind's creator (I kind of share those sentiments myself) but I also absolutely love the Engineers of this film. The way the movie plays around with such concepts as 'God', 'creation', and the ultimate purpose behind our lives and our very existence is vague (occasionally frustratingly so) but, for me, it really works.
Most of the core themes of the movie all seem boil down to one single exchange of dialogue:
Charlie Holloway: What we hoped to achieve was to meet our makers. To get answers. Why they even made us in the first place.
David: Why do you think your people made me?
Charlie Holloway: We made you because we could.
David: Can you imagine how disappointing it would be for you to hear the same thing from your creator?
Charlie Holloway: I guess it's good you can't be disappointed.
The way I look at it, Prometheus is essentially Mary Shelly's Frankenstein in space (pfft, and to think Ridley made a comment about Frankenstein not being an inspiration for Prometheus). Both stories are heavily inspired by the original Greek Prometheus mythology, albeit on different scales, and it definitely shows in the final products. While Frankenstein is a personal take on this philosophy, Ridley Scott's Prometheus is a more grand retelling of the original tale of creation and destruction. The Engineers (humanity's original creators) are Victor Frankenstein reincarnated and we humans play the role of the misunderstood but savage monster that our creator wants to destroy. But in Prometheus we also seem to have a bit of a Frankenstein-complex in ourselves as well; while we are merely a creation (perhaps even a failed one, seeing as we are 2000 years overdue for extermination) we are also creators ourselves. Not of biological life, but of thinking beings nonetheless. And these mechanical lifeforms (one of the most fascinating elements in all three of Ridley Scott's science fiction films) too share with humanity and Frankenstein's monster the need to destroy and make a name for themselves.
Elizabeth Shaw: What happens when Weyland is not around to program you anymore?
David: I suppose I'll be free.
Elizabeth Shaw: You want that?
David: "Want"? Not a concept I'm familiar with. That being said, doesn't everyone want their parents dead?
David 8, like Ash and (Alien), Roy Batty (Blade Runner), and even the non-humanoid Hal 9000 (Stanley Kubrick's 2001: A Space Odyssey) before him, represents the pinnacle of human achievement and innovation, blurring the line between what we call true life forms and mere machinery.
Tyrell: "More human than human" is our motto. (Blade Runner)
Like the Engineers and Victor Frankenstein, we too are meddling in forces beyond our control. Flash forward from Prometheus to the first three films in the Alien franchise. No longer satisfied with simply creating life, we as a species are also constantly on a quest to discover and create new ways to take life. Weyland-Yutani, the merger corporation formed sometime after the events of Peter Weyland's quest for a God-like status and eternal life in Prometheus, spends the entirety of the three films attempting to get their hand on the Alien creature (a creature that, given the less than welcoming status of the facility on LV-223, the Engineers themselves could not even handle as they too tried to utilize the creature's essence in their very own impossible-to-control bioweapons) in order to create weapons. When the last Alien is destroyed in Ellen Ripley's ultimate act of life-preserving self sacrifice in Alien 3 (sacrifice is another huge theme in Prometheus and is responsible for the creation of human life) the Weyland-Yutani corporation's successor, the United Systems Military, actually clones and recreates the beast, all the while manipulating, humiliating, and ultimately destroying themselves and the creature that they could never even dream of actually controlling or containing, let alone converting into a weapon. As if by deliberate design and careful planning, we failed just as our god-like creators did thousands of years ago.