I'm late to the party and I haven't read all 26 pages. So forgive me if what I write was handled on page 5 or so.
I think the explanation for the movie is much simpler than what people are trying to make it out to be. I interpret the film in light of the other Alien films and the motivations of the characters in those films as well. In the Aliens movies, the premise was always the same: Take a group of unwitting humans and place them in proximity of the Alien for the purpose of 'research.' The motivations are greedy and unethical, but consistent. In Alien, the Nostromo is sent to the alien spaceship with the understanding that the crew members would get infected by the Alien species and it was Ash's responsibility to get the specimen back to Earth. Riply ends up foiling the efforts however. In Aliens, the ante is upped to building a whole colony on the planet, again, for the express purpose of getting the inhabitants infected by the Aliens to see what happens. Then the Marines are sent in to, unwittingly, get a sample back. Again, thanks to Riply and an underestimation of the Aliens things go wrong. I believe the third movie is not canon and I haven't seen the fourth, so I'll stop there.
My point is that humans were interested in the xenomorph for the whole purpose of studying how it interacted with humans. There's an idea that it's for weaponization.
Now let's go to Prometheus. The Engineers find a life sustaining but otherwise uninhabited planet and seed it with their own DNA. That takes root and, over the course of millennia, humans evolve. Humans are, genetically speaking, identical to the Engineers. For what purpose would they do such a thing? For the same basic motivations in the other Aliens movies. They were creating a petri dish upon which they could safely test on copies of themselves. People seem to be stuck on the premise that the Engineers were intent on destroying mankind. I don't think that's the case at all. If they wanted to simply kill us, there were easier ways. Rather they wanted to experiment on us. We, being genetic copies of themselves, would give them the answers to what their mutagenic substance was capable of.
Now this didn't go as planned. Somehow the substance got loose on planet LV223, creating monsters which killed the inhabitants. This happened 2,000 years ago, and I think people are making too much of that number. It corresponds (roughly) with the blossoming of civilization across the Earth, but remember that the Aliens work on a glacial pace. Think of how long it took for man to evolve from the initial seeding and 2,000 years is about a minute's worth of time.
Everyone assumes that the Engineer was hell-bent to get to Earth and destroy it. Why? Could it simply be that he just wanted to get the hell out of dodge? Impossible to say. Especially because we do not know what David told him.
Regardless, it seems clear to me that the goal of the Engineers was to experiment on Earth, not destroy it. We were an artificial life form created by their scientists that could be used 'ethically' for testing purposes. At around 2,000 years ago, we had evolved sufficiently for them to conduct their tests and therefore, they prepared the mutagenic goo for transport to Earth. I think this makes much more sense than this highly evolved race just being bitter and angry about killing Jesus, or some such nonsense. If that was the case, they would have just killed us all off and started over. In my opinion, the Engineers had exactly the same motivations in Prometheus as the Corporation does in the later Alien movies.
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