The "sacrificial Engineer" by the waterfalls. This scene, to me, smacked of a near religious zealotry. Who else would don robes and ritualistically swallow a dangerous substance? This Engineer sacrifices himself (itself?) to seed Earth with his DNA. Another thing I thought might be tossed aside is this trope that an entire alien race would be homogenous somehow, nearly identical across their entire planet. What, only humans have any kind of physical diversity? I think it's unlikely the entire race of Engineers looks like this, so between the ritualistic robes and his appearance, I assumed this was a particular faction within the race. Perhaps technological zealots or weapons extremists. Who knows? They're aliens. Since this is science fiction as written by humans, however, it's safe to assume a certain shorthand that ensures we understand the story. I'm going with zealots.
The "black goo." Time and time again, I've seen arguments along the lines of "DNA doesn't work like that" and "there's no kind of super-fluid that would do that." I have two responses to that. 1) this is make-believe and I'm certain an alien race that predates our evolution might have this figured out. 2) what the hell, the black goo is a solution of nanites. That's a good enough sci-fi explanation for me. Once introduced to, let's say, a carbon-based life form, they go to work reorganizing everything.
The "star charts" at the archeological digs and FTL travel. Lighten up, people, it's sci-fi. No kidding, four or five dots does not a star chart make. Yes, even the nearest star system would take more than a couple of years to get to with sub-light drives. One more time: sci-fi. Why has no one complained about the artificial gravity on the Prometheus? Because we're used to seeing that in sci-fi. There are way more laws of physics being broken in sci-fi movies than the petty few you science-y nerds keep coming around to. Give it a rest.
Holograms and briefing meetings. How did Weyland's hologram know where to look? It's 2090. Do you think an iPad might seem like a magical device to someone from 1930? Gosh a-might, how does it know I picked it up? It's a Satan device! Get your head out of your ass.
Skipping orbit, going from space travel to VTL flight. Yes, this is bullshit. No kidding, they should have scanned from orbit, sent probes around the planet, and dropped robotic rovers to take a look around. Man, that would have been incredibly boring. It's sci-fi. Move along. How about the fact that they break atmosphere and Halloway spots what looks like a landing strip? Utter nonsense, for sure, but I haven't seen anyone bitching about that because we're used to it in sci-fi. Whatevs.
No real scientist would behave like that! Yup, that's right. Dr. Asshat breaks the seal on his helmet as soon as they realize there's oxygen. That was dumb. The biologist isn't at all interested in a 9-foot tall dead body, but he wants to kiss the black water penis worm. That was dumb. Both of those scenes could have been fixed with a tiny re-write. None of these folks are behaving like scientists at all. Why aren't they adhering to the same rules as other fictional scientists? Wait, they are. This is not "hard" science fiction. I forgive you, sci-fi fantasy. (Still, they were lousy scientists. And fuck you, Jar-Jar Binks.)
They mapped the tunnels, how did they get lost? They got lost because they took a wrong turn. Yes, they were in contact with the ship, but when the scene cut back to the bridge, the diagram was still under construction. They only got lost long enough to get trapped. Remember? They were stupid. It happens. I bet you were stupid just yesterday. Luckily it didn't cost you your life on an alien planet.
What exactly is David's motivation? He doesn't have motivation. Weyland built him. He does what Weyland wants within the context of his crazy android brain. Weyland refers to him as the "closest thing I have to a son." I bet that pisses his flesh and blood daughter off. Maybe that's why she's so dismissive and downright brutal towards David? Maybe she had to grow up with this thing and resents it. I know I would've. There's a long-running tenet in sci-fi that if you're going to build a robot brain that can think, you'll need to "grow" it. Maybe that's why David is constantly learning and practicing when he's alone. In this instance, no, I don't think they could just "download" everything into his brain. In fact, I considered David to be a parallel construct for the Engineers relationship with humans. Some of the shit David says clearly frames his state of mind toward humans, his inferior creators.
What was the blue goo that David found? Who gives a fuck? It was an interesting bit, like the egg buttons or the flute controller or the glyph controls. Maybe it was motor oil.
Why do the Engineers want to kill us? I don't think they "want" to kill us. We're the running bathtub, the boiling kettle on the stove, an experiment allowed to go on too long. These zealots created the black goo to reconfigure DNA. The first reconfiguring eventually created humans, the second creates an extremely hostile organism hell bent on reproducing or killing. We're intended to either be incubators or catalysts or a test run. The Engineers have created a weapon that is part virus, part gun. Who knows what their motivation was, but I suspect this nutjob group had it in for some other part of their race. Our DNA matches theirs, so the goo affects them too. When the crew of the Prometheus sees the recording of Engineers running like hell, maybe one of their own got infected. I can see how it might throw things off on the base. When they awaken an Engineer, he's all freaked to see their little lab test all grown up and in his living room. Holy shit, they came to us, bro! How long was I asleep? I damn well better deliver the payload, let's get phase 2 the fuck going and clean these monkeys out. Hold on a sec while I step on these cockroaches... And we don't know what David said to that big boy. Maybe he cracked wise on his momma.
Auto-cesarian warm up for marathon. Dr. Shaw initiates a self-cesarian to extract an alien squid thing from her body. Neat. How is she still moving? Considering the copious amount of drugs-from-the-future she kept injecting herself with, I'm guessing that's the answer. She also pulled on a skin-tight suit from the future which, I guess, is helping to hold her together. Yes, yes, yes, I know: when we conduct an abdominal surgery in 2012, we cut all the way through the muscle walls to get at and extract shit leaving the patient severely hobbled. Maybe eighty years from now it won't be as physically traumatic and the procedure may be performed by a fancy-ass robo-medic? Sci-fi! She certainly acts like she's in a great deal of pain until the very end when she's hauling David's busted body around. I'd score that 'even' on a sci-fi scale.
Why do they run straight when the ship is falling on them? Better question: why didn't the goddamned ship crumple when it fell from the sky and hit the ground? It's a tough bastard, no? Wait. Why didn't the Prometheus just crumple against that tough bastard? Yeah, don't think too hard about it, just run. The cut scenes of the two women running do show them zig-zagging a bit then heading in different directions as they split up. One of them chooses wrong. End of story.
All in all, it wasn't the most vile piece of sci-fi garbage I've ever seen. My point is that it wasn't nearly as bad as so many people put on that it was. I think the bigger questions about the story's concepts were answered sufficiently, but a number of the characters and their behaviors and motivations were clearly flawed. If we're going to bitch about a sci-fi story, bitch about the story and not the sci-fi, there's too many easy ways to concoct an answer for science fantasy. How come no one's asked why flamethrowers were brought along as weapons for an alien atmosphere. How does that work?