Addressing John's points from the post you linked to:
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1) Why is it assumed it is an invitation to the stars - and as has been said already, whether it is or isn't, why do the co-ordinates lead to a secret arms dump?[/quote]
I thought the whole point was that (mirroring the Prometheus myth) the Engineers were seeking to punish humanity for trying to get too close to their creators. Presumably those 'invitations' were created millions of years after we see the first Engineer create life on Earth in the opening sequence - the logical implication is that the Engineers came back to Earth at some point with the explicit goal of leading us somewhere very nasty once we got smart enough to have the technology to get there.
It reminds me a little of the function of the moon-obelisk in "2001", which acted like a cosmic alarm system to let the aliens know when we'd become smart enough to get to the moon.
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2) Why exactly IS Weyland's presence a big secret. I mean, it works as a story 'reveal', but really he wants to meet with an alien. Why would his presence, in statis for the most part, be such a secret practically within story logic?[/quote]
I'm not completely clear on this, but I'm guessing that he'd rather make out that he's funding the project as a purely exploratory mission of discovery, rather than as a self-centred personal venture of his own. I agree, though, that the reasoning was a bit vague on exactly why he wanted his presence to be kept such a secret, and why David assumed he wouldn't want their dream-conversations to be shared with his daughter.
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3) The ghostly holograms replay old events(why do they exist?)[/quote]
I just saw that as an alien CCTV-type thing that David had worked out how to operate. Seems pretty reasonable if it's an experimental weapon development facility that they'd have recording capabilities, especially if something went wrong.
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We see that a massive stone door severed an Ancient Engineer's head cleanly off their shoulders. It's amazing that a door that seems to be that thick can cut so cleanly rather than just squishing the head.[/quote]
I didn't register the thickness of the door at all, so that didn't occur to me whatsoever.
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Mind you, we also get a pointless re-animated head explodey scene later that tells us... well, nothing.[/quote]
Well, it tells us about the deadly infection, which is pretty important.
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4) Hello, scientists... you see a strange alien life-form in what you think is an alien tomb with weird things happening in it and you want to get down on all fours and play with it? You deserve to die. And, yes... voila.[/quote]
Like I said, that's the touchy-feely biologist getting his just rewards. Yeah, most people might not react like that, but he's established from his very first scene as being the kind of person who might.
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5) We learn Rapace's character can't have kids and how frustrating that is. BIG DEAL scene. Immediately after we find out she's pregnant. There's surely an opportunity for a moment when she'd consider keeping the child, even if confounded by the pregnancy.[/quote]
Interestingly, I read that completely differently - that if she knows she's medically incapable of having children, she'd be even more weirded out by having been successfully impregnated by an alien seed.
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If David has a plan to put her in stasis take the organism inside her back to Earth, why does he deliberately antagonise her about the unhealthy nature of the embryo so that she'd obviously NOT want it? The story beats just feel very off and David's agenda isn't clear or his technique sucks.[/quote]
Yeah, that's a bit odd, isn't it? I assumed that the plan was to take a healthy alien foetus back to Earth in stasis (a bit like in previous Alien films).
But presumably, given David's behaviour - and also that he didn't give Shaw enough sedative to keep her inactive - he didn't want that to happen. Maybe he had a completely different plan. I'm not sure about that one at all.
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6) Why are the captain's men (the betting duo, whose names I can't even remember) so willing to 'go down with the ship'? There's really no POINT in them dying and I've seen no huge demonstrations of loyalty or suicidal tendencies from them before that.[/quote]
Yeah, I feel as though those characters were under-served by the movie. I wonder if we'll see more of them in a director's cut. Them wanting to go along with Idris almost felt like a gag - as though death would be better than being stuck on an alien moon with Charlize Theron's character. It certainly felt a bit unnecessary.
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6) Charlie Theron's character dies a stupid death because she can't outrun the long shadow of a falling massive elongated spaceship. Rapace's takes two steps to the left and voila, safe (well, for a moment) Again, there's a metaphor there.[/quote]
OK, maybe that was a bit stupid

. But in fairness, they did have Theron's character trip over and so end up a lot closer to the ship bearing down on them than Shaw was...
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So yeah, it's not a flawless film, but I feel like most of those things are still nitpicks that don't take away from the larger themes being played with, and don't break the plot.
[quote name='steveuk' timestamp='1339276573' post='2443746']
I get that as an idea, but... in context it's moronic.
Whatever his "character" the biologist shouldn't be stupid enough to approach the 'cobra' and the geologist shouldn't be such a coward if he got on a spaceship in the first place![/quote]
Well, they were both in pretty extreme circumstances. I think the biologist's curiosity probably got the better of him to an extent. And the geologist - who's only in it for the money, and is probably a lot less macho than he would like people to think - probably would have never expected to be stuck in an alien building away from most of the rest of the crew and surrounded by alien creatures.
It really didn't bother me that much - I don't really know what else they could have done, given that they were already scared that a creature was prowling the tunnels. They were in a bit of a pickle and reacted a bit stupidly - I don't see it as particularly unfeasible.