I think I'd heard enough bad reviews that my expectations wer lowered and I wasn't actually that disappointed. But I totally agree with everything C_S is saying: so much didn't make sense. And not in a purely confusing way--more in a "characters are introduced with motivations that conflict with later actions" sort of way.
Okay, maybe I was purely confused by why they put Guy Pearce in unrecognizeable Freddy Krueger makeup rather than using a more age-appropriate actor in more reasonable makeup. But that's just me.
The main thing that bugged me, however, was the storyline of the Engineers creating life on earth. Not for personal religious reasons or anything, just because...what's the point? Think about Alien: so much of its brilliance is that at the end, much of the mystery is intact. The draw to Prometheus is that we might find out what the fossilized alien in the original was, and if it randomly encounted the xenomorph like the humans did, or if there's a greater relationship (no way I was going to miss that).
So the way they explain it is that the dead alien's race CREATED HUMANITY!? And that the xenomorphs are a biological weapon meant to destroy us, presumably because of some transgression? And later on, the Nostromo (also a Weyland ship) is going to randomly answer a distress beacon from a derelict ship belonging to these very same aliens with a xenomorph that humans now had a hand in creating?
Shut up.
I mean, I hear there are two movies between Prometheus and Alien that may connect the dots, and I don't know who has the greater story credit here or and where the line is between Ridley Scott and Lindeloff: but this feels like a Lost-type progression. Where something with unbelievably tight mystery and suspense in the beginning is allowed to spiral into a quasi-mythological universe where confusing plot points are glossed over because of "meta" concerns.
That's the part that disappointed me. There's so much room to expand the story within the existing framework (the alien and its civilization, the xenomorph, the Weyland company, human society at the time). Why put all this other stuff on top of it?