Spoilery warnings still in effect.....
The Engineers; we never did get a good idea of their motives. Did they come to Earth to create life or destroy it or for something else and we were just a side effect? Why come back to destroy us? Had we done something other than what they wanted or were we not what they wanted? And either way, why bother with us rather than just start over somewhere else? Either way, what was their goal? Their end game?
My general comment is that I guess to me, I didn't need to know all of this. If humans come in contact with aliens for the first time, which is sort of what this was, shouldn't
it be somewhat confusing and ambiguous? I found that to be a strength, not a weakness. Plot holes are one thing, but not understanding an alien's motivation isn't something that is a problem to me.
The Engineer who tried to pilot the ship off the planet appeared to be somewhat different than the Engineer who appeared on Earth. Was that just evolution or had they been trying to alter themselves and had it partially succeeded? Was that why we got an early Alien from the Engineer while Shaw popped out a facehugger? Because, if we had the same DNA, why would we see the start of an acid-blooded, silicon-based life form spring from something based on a carbon-based life form? Holloway to Shaw to the Engineer?
We don't even know that it was Earth at the beginning. Could have been any planet, anywhere. Are they weapons manufacturers or gardeners or something else entirely... that's the fun mystery to me.
What did David know? By the end it seems like his goal was supposed to be to help Weyland meet the Engineers but up to the point we know that, he seems to know more than anyone else about what to expect on the planet. Why the experiment with Holloway? Did he read something or know something more about what the Engineers were doing on the planet? If his real goal was to get Weyland a face to face, why all the off-book stuff? Also, what did he say to the Engineer at the end? Maybe I'm forgetting now, but I didn't think that was explained either.
David should have known more, he more or less figured out their language. As for his motives... there was a whole subtext about destroying or being dangerous to your creators / wanting to be free of your creators. David embodied that for humans the way humans do for engineers. I agree that it would have been nice to know more of what David was doing, but unclear motives and how to react to them is a key theme for the movie.
Then there was Captain Janek who, with one visit to the labyrinth, suddenly knows that it's a military installation and not, well, anything else. Maybe that's just deductive reasoning, but the movie seems to make it a key point that we now know this.
His opinion, and given Ridley Scott's comments over the years, probably the right one.
What was Meredith Vickers really up to? She said early on that she was there because the Weyland corporation was laying out a lot of money, but what CEO would actually go herself on some mission like this? So was she really there just because she was the boss or was there some other reason that we didn't know about? She didn't seem to know that Weyland himself was there yet she had that medical table in her section of the Prometheus as if she knew something we didn't. Or, I guess she was just paranoid...but that brings me back to why she would go herself.
My guess, to make sure her father didn't come back, like David... again, the motif of getting free of your creators even if it means destroying them.
What effect did the black ooze have on Holloway and Fifield? It apparently broke up the Engineer on Earth and the worms became some type of...something else. But what were Fifield and Holloway becoming and how did the ooze change Holloway enough that he could plant a facehugger in Shaw? Again, this comes back to what the Engineers were trying to accomplish with the black ooze, something that we don't have any answers to.
I've read some good theories that the ooze reacts to your intent... it's as good as anything out there, and if you read the movie in those terms, lots of it fits together in terms of the ooze.
It felt, to me, like the entire movie was more set up than anything...like we need to get a sequel out of it in order to really find out what was going on.
Sure, and there are talks of a trilogy... but if it ended here I'd be happy with it as a mysterious first-encounter type of story.