Here's my problem with the "mystery" and "questions" raised in Prometheus. Feel free to disagree, but this is how I feel.
There's nothing wrong with unanswered questions or mystery in movies, as long as they're not at the centre of the story.
Take Alien - there is the unanswered question of the derelict and the space jockey, but the story is focussed around the Nostromo crew and their fate, so the these questions have no direct bearing on the characters or the action that follows; the growth of the Alien is central and the Space Jockey is a tiny little tangential question.
In Prometheus, however, all the mystery has been pushed to the centre of the story. All of the characters' and the action revolve around unanswered questions, which ends up being profoundly unsatisfying to some audience members. It is - I think - deeply frustrating not to be able to grasp the motivation of a screen character, even by the end of the movie, because it is 'shrouded in mystery'. What you sense, as an audience member, is that the writer has no clue. And the idea that one would need to trawl through hours of extras or commentary on a disc released months later, just to understand what the film was about, defies logic.