I'm going to complain about Prometheus some more. I've been hung up on the stupid characters, but that's not the problem that bothers me most.
There are good stories to be told about stupid characters: General Custer, Enron, Arthur Anderson, etc. You can tell good stories about otherwise smart characters working on faith or interpretation that turns out to be very wrong (Star Trek V, Stargate). You can tell good stories about super villains that overestimate their own strength and underestimate their opponent's cleverness or physical strength (Loki, or Vader). You can tell good stories about wtf mysteries that are never answered (the monolith in A Space Odyssey). You can tell good stories about characters that never change, or about space captain characters only interested in money who seemingly make a moral decision at the last moment (Han Solo).
But you can't tell a stupid story about stupid characters and expect it to hold up. I'm imagining Scott or the writers of Prometheus saying in interviews "You should see what we left on the cutting room floor, then it would all make sense." And it's as if they wrote the story based on trailer moments ("You know what we should have? A protagonist who realizes she was *so* *wrong*.") As if stringing together dramatic moments makes a good story. You can't just dump Han Solo into a scene and expect it to flow. You can't have characters speculate on no evidence and then use their conclusions as exposition, making their assumptions a story reality. In any other movie, "This star map suggests we're not alone in the universe." In this movie: "This star map shows that aliens created our DNA!" and then it's true. "This is a military installation." and then it's true.
As far as I can remember, Shaw was never present when the black goo was active - was she with the group when she saw the canisters? She never saw the cobra, never knew that David poisoned her boyfriend. Set this story in 19th century Egypt and you've got two explorers opening up an Egyptian tomb, removing their gas masks, getting infected with Hanta or Bubonic plague virus, transferring the infection to each other, then assuming that undead Egyptian mummies are out to convert them and take them to the underworld.
Do a checksum; tell this story from the point of view of the Engineers. They seed the Earth with a quarter cup of juice to create humans, make multiple trips back to Earth to paint an invitation to their home military installation, then for shits and giggles create a bioweapon with a plan to go back to Earth and wipe it out, store it both in multiple tons of leaky canisters and arranged in ceremonial form in front of their big idol head, put themselves into stasis but accidentally get infected with the bioweapon (and this exact situation happens in all the other pyramids in Engineer valley), get woken up by a (for all he knows) human that communicates his language in a friendly manner, freaks out and instead of analyzing the situation or concerning himself with further contamination thinks to himself "I must finish the mission immediately and go wipe out Earth, nevermind my need to go into status," and then "I must kill every human here immediately."
That's the story they were trying to tell?