I think the main theme of this film is "sacrifice for preserving/creating life versus preserving you're own life at the expense of others lives". The sacrificing theme is apparent from the beginning of the film, right up to the end with Jarek and his crew sacrificing themselves to save life on Earth. Could make an entire post just about different examples of this throughout the film.
The black goo. I fully believe that the good ingested by the Engineer at the beginning of the film is the same that is found in the vases. The goo creates life by destroying the host. We only see the goo clearly ingested twice in the film. The Engineer who takes a huge dose at the beginning of the film, and Holloway who has a small drop of it in a drink. The Engineer falls apart right away to create new life, Holloway on the other hand only had a drop... and he starts to die as well, but doesn't show ANY symptoms of anything being wrong until AFTER he empregnants Shaw. So my theory is, after he created new life that's when he started dying, just like the facehuggers in the original Alien and like the giant facehugger at the end of this film.
So the black goo isn't really WMDs, there more like a giant reset switch for a race. So the other question is if the Engineers created intelligent life on Earth, why would they suddenly decide to start over. We're actually given a hint to this. We know they were about to leave to get this done before they were all killed and we know that this event happened roughly 2,000 years ago. What major event happened on Earth roughly 2,000 years ago? The birth of Christ? The Crucifixion? Maybe Jesus was an emissary for the Engineers to steer us in the right direction and we crucified him. Before anyone tells me I'm off base keep this in mind. The main character of the film is religious and wears a crucifix, the bulk of the film takes place on Christmas day and Shaw's closing entry not only does she mention the year, but says specifically "in the year of our lord 2094".
I didn't even start in the whole Annunaki and Sumerian thing, or the whole Prometheus thing (the Titan, not the spaceship)... there's surprisingly a lot you can get into here seriously. Ok, enough for now.