Spoilers:
It seemed to go downhill as soon as Elizabeth found out she was pregnant and escaped the room she was in to have that machine remove it. Shortly after, Janek is telling Elizabeth about the planet being a research station without acknowledging what happened to her at all. From what I can remember, not one person mentioned it. She even had to knock out people to escape the room, if I remember correctly.
Elizabeth has a knock down drag out fight with several crew members, then has an alien fetus removed by a robo doctor machine. But it's fine, nobody else even comments about it later, and the people she fought with and ran away from seem to have forgotten it happened.
Similarly, when 2 people get attacked by mutated worm creatures the rest of the crew needs to investigate in person. You know, because the equipment on a trillion dollar starship that's been monitoring suit cameras and basic health functions lacks basic DVR features and wasn't designed to sound an alarm when someone dies or their heartbeat indicates a medical emergency. Just plain dumb at a foundational level.
Perhaps we, as a species, weren´t simply done yet. Something still had to burst out our collective chests in order for us to actualize our genetic potential. Maybe the xenomorphs were the ultimate monkeys out of which the definitive mankind would evolve from.
Piss poor execution though.
Instead, they poured an immense amount of design skill into the sets and backgrounds to make a wonderfully beautiful movie. And they built up this tremendous premise and a fantastic universe. And they populated it with several truly deep and rich and wonderful characters. And they had those characters acted by outrageously talented actors (Charlize Theron, Michael Fassbender, Idris Elba, Guy Pierce).
And then they pissed it all away with a shoddy plot and incompetent direction.
Spoilers follow:
The engineer turns out to just be a dime store monster. Nobody's actions are interesting, meaningful, or seem to flow from any significant motive other than to conform to the plot. One of the most dramatic scenes in the movie (when Janek decides to commit suicide by ramming the engineer's ship) comes off as completely anti-climactic because it comes out of nowhere. Similarly, the major revelation of the movie of the planet being a biowarfare research station comes out of Janek's mouth but it is so out of place and out of character that you can almost hear the clanking boilerplate of dreaded exposition falling into position. Perhaps the most interesting character of the entire movie, David, remains nothing more than an automaton throughout the movie with only a gnat's whisker of a hint that he is anything more.
Prometheus the fictional spaceship is a "trillion dollar" mission which is unaccountably staffed by a handful of incompetents, fuckups, and pseudo-villains who throw away their lives for the silliest and least meaningful of reasons. It is an apt metaphor for the movie itself.