The answer to some of the questions from numerous articles on the BluRay deleted scenes...
The black goo is
pure xenomorph genetic material that seems to either break down (first scene) or hyperaccelerate the genetic structure of the individual, and combine it with the environment, or if there is no exterior environment present, with its own alien patterns. Perhaps there are two types of goo out there.
The Engineers take the goo and seed the universe as a kind of ritual sacrifice. Again, this isn't explicit, but it seems they do it because they can.
All the Engineers
are dead because their xeno-goo turned on them (in the throne room, there are holes in all the other vacant tubes...around the chest area), and it was set on probably by another
Engineer, who might have been impregnated, escaped, and reached LV 426.
Milburn's an entomologist (studies insects), and so loves snakes and doesn't mind baiting them. (Still stupid though)
Holloway is grumpy because he wanted live engineers and is so, pissed off when
the head explodes from infection.
Weyland was behind David's machinations, and together, they used the crew as guinea pigs to see what the goo did (except it seems David has ethical programming, thus Holloway stating that 'anything and everything' is permitted to find the answers for what they came for, gives him permission to spike his drink with the goo)
Guy Pearce was cast because there was a dream sequence scripted involving David and his 40 year old self that wasn't included.
isn't a robot.
The Engineers and Weyland had a brief conversation in a deleted scene about how he is a 'God' for creating David - and whilst this isn't explicitly stated, perhaps this is why they got sick of man trying to run the show and turn all serial killer.
The Captain and Vickers ended up hooking up due to the fact they had a few deleted scenes involving flirting that were prior to that scene.
He then later
sacrifices himself quickly because he had a military past which involved his running foul of a contamination outbreak, and knows the consequences of inaction.
This answers some but not all of the questions here: http://www.juliansanchez.com/2012/06/11/whats-wrong-with-prometheus-a-partial-list Most questions are either due to sloppy plotting, or just overemphasis on the thematics: life, creation, father vs son, identity, purpose, origins and final destination, the unknown, the insignificant nihilism of creation and destruction, loss and transcendence, and religious mythology...the only difference is Alien didn't make us *have* to think in order to explore its' own logic.
My old and very extensive review is at the top of page 5. http://www.icheckmovies.com/movies/prometheus/comments/?page=5