I liked Prometheus for what it was, even though the second half was an absolute mess (full of shoddy editing/pacing and gaping plot holes--I always point to the C-Section sequence as an example. A terrific scene, bookended by two of the absolute dumbest moments in the film that almost completely take me out of the film. Oh, Shaw just ran off to go abort her alien baby. Let's just let her do her thing IN WEYLAND'S MED POD, no harm no foul. We'll just use the time to wake up Weyland WHO IS TOTALLY ON THE VERGE OF DEATH AND MIGHT NEED THAT MED POD UPON WAKING UP. Oh, and we won't bother seeing if the alien baby survived or not. Or studying it. Or anything.).
I liked the Engineers, but as their own thing. I wish that they weren't the Space Jockies, that they weren't human. Prometheus did rupture the thematic ground on which Alien stood. It did it with extremely interesting ideas, things that I still would like to see further explored, but I would have preferred it done another step removed from the world of Alien. Incomprehensible cosmic horrors, by very definition, shouldn't have to be relatable, let alone human.