One wonders how Ridley Scott made both the original Alien and Prometheus. What Prometheus did right: the filmography and sets were fantastic. Some actors turned in incredible performances, e.g. Michael Fassbender, Noomi Rapace, and Idris Elba.
What they did wrong: terrible make-up for Weyland, he looks like his head was dipped in wax and they called it a day. It asked questions that it never answered. It showed characters doing incredibly stupid things, like running into a corridor alone when there was approaching danger, or getting trying to pick up a space snake. And its sequel was even worse - killing the main character off-screen, people running around an alien planet without protection, splitting up teams into small groups that can be easily killed, etc. Ordinary people aren't so stupid, let alone a bunch of supposedly highly trained professionals facing an unknown threat.
BTW I should add another sci-fi movie that has largely been forgotten: Event Horizon.