Everyone makes insanely stupid decisions or is prevented from making a sane decision by some other moron at every opportunity. It's like everyone on board the Prometheus didn't want to be there, didn't care they'd found alien life or (ugh) possible origins of human life, and actively sought death at every turn. Except for Theron's character, who had the few brain cells the crew could scrape together, was capable and clearly wanted to live.
I thought a huge error was made in putting so many characters in play and then setting up Noomi (who isn't that good) as the clear heroine with a character shield from word one. She should have died about half way into the film suddenly and with great violence, so that Theron's character (the justifiably paranoid asshole who couldn't get along with anyone) could step in and try to salvage the inevitable disaster, if only for herself and maybe the audience would have been surprised at a turn the film took.
Elba, Theron and Fassbender were all good, but they weren't given anything to work with. Noomi was meh. Her boyfriend was lame just like he is in every movie he's in and the rest of the dozen other characters are ciphers, with little or no dialogue, only there to hold up the sets and then die.
As for the deeper message? Engineer Aliens are assholes. And humans are assholes to robots. That's it. Having characters say there are Big Things out there that need Big Answers is not the same as actually having those characters explore those Big Things or find those Big Answers.
I'll give it one more go with a Director's Cut (Kingdom of Heaven DC is frickin awesome compared to the wreck of a theatrical release).
C+ (Leaning towards C/C- as time passes)
Yeah now that would have been interesting. You are not the only person who would have liked to see more development with Theron's character as the only one who didn't really deserve what they got. If Noomi had been placed in stasis and Theron had to step up, that would have been a WAY better finale. Theron could work the doctor bot (far less silly) and they could have worked towards several characters with potential for development surviving to the end (or not)