First and foremost, I enjoyed 'Prometheus,' despite it's flaws. It was magnificent, confusing, epic, other-wordly, yet unsatisfying. The production values of 'Prometheus' are visually stunning. Ridley Scott is Ridley Scott for a reason. Overall 'Prometheus' is a haunting, heavy, introspective film, so much so that it breaks under it's own weight. The film needed some fleshing out.
My main beef with 'Prometheus' is the writing, specifically the gaping plot holes. The main writer of 'Prometheus' is John Spaihts, who wrote last year's B-movie, 'The Darkest Hour.' From what I've read, Spaihts wrote 'Prometheus' strictly as an 'Alien' prequel, which would have been adequate, but not necessarily epic.
The soulfulness of 'Prometheus' can be attributed to 'Lost' writer Damon Lindelof, who likely introduced the deep and grandiose ideas of the film. That said, sometimes you have to take the good with the bad. Unfortunately, Lindelof likely introduced the pretentious and baffling aspects of 'Prometheus' as well. The 'Lost' writers are known for their brilliant, ambitious storytelling. 'Lost' writers are also known for cluttered scripts, superfluous flashbacks, and plot holes. Unplugged plot holes are the main culprit in 'Prometheus.'
I have been able to address most of the plot holes in 'Prometheus' to my own satisfaction, but the writers shouldn't make the audience work this hard to do their job. Mysteries are good, but everyone wants a satisfying conclusion, even if the mystery is ongoing (i.e. 'Inception' is a perfect example). The writers could have done a better job filling in the gaps with just a few additional scenes. Perhaps there will be a director's cut with additional footage to fill in the blanks.
See my take on all of the unanswered questions in 'Prometheus.'