After watching the movie I don't think is a masterpiece but it is a great movie and the beginning of the Prometheus series.. which eventually will also shed some answers on the Alien series.
I think people here are very concerned with the link with Alien, the only hint in the movie is how Xeno is first formed, but the link to Alien is still to come.
Now my thoughts on Prometheus.
I think the Engineers inhabit five solar systems, as there are five circles in the paintings of the ancient civilizations. I think there is a great war going on, not sure if it is civil or with other civilization. The Engineers deliberately created life on Earth, they created us to use us in one or other way, just same reason why we create robots. They want us to be an army. By the time of the ancient civilizations they check on us and they see that we are intelligent beings and that we have reached a certain technologic degree, but not strong enough to be soldiers in their dream army.
Now they are running a series of biological experiments in planet LV-223 with the eventual aim of transforming humans into these super creatures, but with the misfortune that all beings created are very hostile and kill all engineers in the planet, but one. The engineers in planet LV-223 are also in charge of the experiment in earth and because of the great war going on, Earth is forgotten.
When the humans awake this engineer the engineer feels threaten by us, after all we are an inferior specie created by them and now we are capable of space travel. This why he attacks the crew.
I have thought other storylines but this is the one that makes more sense to me.
Another storyline would be that the Engineer leader is the one who comes to earth and the one who destroys himself to create life. But the rest of my thoughts here are not as consistent as before.
