The trailer for the PROMETHEUS Blu-Ray declared 'Questions will be answered'...
I've now had an opportunity to listen to both Ridley Scott's and the screenwriter's commentaries, and here's a summary. I've also seen the deleted/alternative scenes which also add a bit more detail.
1. Jon Spaihts and Damon Lindelhof recorded their commentaries separately and before the movie even premièred. The comments were merged together to form one audio track. Lindelhof is used to being hated (after Lost) and anticipated the abuse in his self-deprecating way. Nevertheless he likes adding mystery. Both acknowledged potential problems and both had issues with the final theatrical release (e.g. whistle password, rapid growth of the fetus, etc). Both writers (& director) seemed scientifically illiterate - whenever they talk about biology or astronomy, they make serious blunders.
2. Ridley Scott delivers a laconic 'phoned-in' commentary - half of which is just describing the bleeding obvious. For the rest of the time, he's being satisfied how well everything turned out. Not once does he acknowledge any problems. In fact, in an eye-opening section between 31min and 33min, he says that anyone who questions his judgement can fuck off - they must be either inexperienced or stupid. He's got 3 movies in the Library of Congress, therefore he's earned the right to be surrounded by 'yes men'. For him, the movie is perfect. But there's no indication that he's into the story or even the genre. It's just a job he does. He repeatedly states how pleased he is in knocking out the movie in 82 days because he doesn't bother with rehearsals, etc. (I wonder if he got a bonus in keeping the movie to 2 hours as he eagerly dispensed with many interesting scenes the writers came up with.)
3. Why did David spike Holloway's drink? Because Weyland implored (from his dream-state) 'try harder' to find a cure for mortality. After Holloway admitted he'd do anything to find answers, David had carte blanche to use him as a guinea pig. (The second law of robotics obviously doesn't apply). David didn't know what the goo would do, nor was there an ulterior corporate motive. (No, it doesn't make any sense why the robot would potentially infect the entire crew simply to see if the goo made you live forever. Ever heard of a lab rat?)
4. Why did the Engineer go 'aaaaaah' and rip off David's head? According to Ridley, he was offended at being addressed by a synthetic being. According to the screenwriters, he was offended at being woken up and addressed by 'chimpanzees' (i.e. us). (yeah, real god-like).
5. Why did the Engineer not talk? In a longer deleted scene, he did talk. But it was felt during editing that speaking removed his god-like aura. Apparently making him go 'aaaaaaah' and act like a WWF wrestler is more god-like. Idiots.
6. Where do the Engineers come from? Paradise. (does that clear things up?)
7. Why did they change their mind in respect to Earth? No one knows. (No one attempted to speculate what threat iron age humans have to any thing else in the universe). If the intention was always to use Earth as a weapons testing ground, then why graffiti our caves?
8. When was the opening sequence set? According to Ridley Scott, 10 million years ago before there was any life. (Which is completely wrong. Life began on Earth at least 3.5 billion years ago. In an alternate extended opening sequence, you clearly see trees and moss as the Engineer sacrifices himself. )
9. Why is the ship in the opening scene a saucer and not the iconic Giger horse-shoe ship? Because their ship design evolved.
10. Why can David speak the Engineer's language? Because he learned sanskrit and other ur-languages and somehow the Engineer language got transmitted in the DNA that seeded life. (Doesn't make any sense, but that's what you get when you have arty people writing science fiction.) No mention that they would have had to come back around 35,000 years ago and scribble on our cave walls.
11. Could staples really work on Shaw's caesarian? Ridley once got his knee stapled, so yes it could. (I'm serious - that's what he says).
12. Was there any significance to "Christmas" or events 2000 years ago? Nothing was mentioned. But the theme of children wanting to kill their parents was often mentioned. Charlize wants Weyland to die. David wants his creators to die.
13. David's motives? The screenwriters spoke at length about David's thoughts towards humans and the Engineers and his own artificialness, but not wanting to go down the Pinocchio route. For all of Fassbender's terrific performance, he actually doesn't convey half of what is supposed to be attributed to him by the writers.
14. Other issues? Ridley Scott repeatedly says that he decided to do something that way because it was cool or 'seemed right'. No explanations. No justifications. Doesn't matter if it doesn't make sense. Sean Harris, the actor who played Fifield the geologist suggested he go 'punk' and Scott simply said 'okay, why not?'. Can you really re-animate a 2000 year old head? Doesn't matter. Just add some techno-babble and it's fine.
In summary, I get the impression Ridley Scott doesn't really care. He's suffering from 'George Lucas Syndrome' (his shit don't stink), and is more concerned with delivering a product on budget, on time for the studio, than pleasing the fans. I did investigate the issue of science consultant, and amazingly the The Science & Entertainment Exchange was used, but only minimally and I can only conclude that most of the scientific advice was ignored.
Had it just been Jon Spaihts original script and had it been given to a director that cares about the material and who listened to a science consultant, it might have been a good movie.
Five hours of Scott telling you how cool his "vision" is and all the actors/crew blowing sunshine up each other.