Hi Wonk,
As you seem to have a fair handle on the vagueness of the movie, I'd appreciate an answer on one question that has been bugging me. I cannot figure it out.
In the beginning the archaeologists find this star map in cave paintings all over the planet from different ancient civilizations. They make the logical (to me) assumption that the aliens want humans to go to that place.
But the story takes a bizarre turn in that they aliens apparently want to destroy humanity???? Still don't really understand why.
My question, if the aliens wanted to destroy humankind, why leave them all these messages on where to find the Engineers?
That question is pretty much the whole point of the movie really, and they spend most of the movie talking about it, indirectly. Probably one of the most interesting scenes of the movie to me was when the android had a conversation with the archaeologist early in, and the archaeologist indicated he had come because he wished to speak to his creator.
The Android told him that he was in that moment, speaking to his own creator. (Humans built him.) Since he had no emotions, it wasn't the same issue to him, but wouldn't he find it terrible if his creator told him that he built him, "Just because he could?"
And that's the actual fruit of it right there, and here's the idea that came to me then, in that moment.
If we made new life forms, we might not really know what would happen to them. We might not actually care that much. We might make an experiment and forget about it. Thousands of years later, our descendents might decide to destroy it. Don't you get it? That's the idea here. So much time has gone by, that their entire civilization is utterly different from the one that actually made us, in this storyline. It makes perfect sense.
If we made such an artificial lifeform, and our descendants found it thousands of years later, why would their reactions to it be the same as ours, we who made it? Would they even think of it as their own? Who knows? The archaeologist made the same fundamental assumption that you did, because he was ascribing a sort of godhood to them. But that assumption doesn't really make any sense if you look at it objectively.
The 'jesus engineer' which was brought up as an idea was never actually put into the movie, and I prefer not to bring it up because it's actually superfluous. The whole point of it is, they don't know.
He went thousands of light years, to find out why his creators made us. And he found out this his creators wanted us dead, and he doesn't even know why. It's extremely realistic, and it made his girlfriend more than a little annoyed too, as you could tell from the ending sequence when she managed to get a spacecraft, and elected to go to another one of their worlds to try to find out what they are doing, rather than go home.