I liked Prometheus, though I didn't love it, and it admittedly fell a bit short of my expectations. I think the criticism leveled at the film that its focus was bifurcated between waxing philosophical and playing as an ode to sci-fi horror was pretty well deserved, since the narrative oscillates between long dialogues regarding faith, science, and creation and grotesque set-pieces. It felt sometimes like I was watching two different films, and though I think these halves were married on a conceptual level--"creation," whether as an act of a god or of science and technology, is oftentimes a fickle, unmotivated, and violent thing--they didn't really play well together on the screen.
I didn't find the film to be too muddled philosophically, as some reviewers have suggested. The idea that the ascension from humanity to 'deity' requires the creation of a technology that is independent and organic, a sentient being is played out in a number of ways, and it ties in with the mythos of the Alien films: omnipotence is paradoxically both gained and lost by creating a truly independent, sentient being; it's gained because giving birth to new life is seen as an act of god, and it's lost because children have a mind of their own, and as David says, they all want to see their parents die. That much was clear.
The problem was that the idea that 'creation' can be the product of a creator's narcissistic whim, that the justification for creating live can be given in the tautology, "because we could," becomes Ridley Scott's cop-out for not tying together or even explaining certain major plot points. We have no plausible explanation for why human beings were made, why they were invited to this place, or why they might now be exterminated through nouveau biological warfare. And that's fine, because it's in keeping with the film's core ontological beliefs, but it still felt to me like Ridley Scott wanted an Alien film and found this an easy way to justify senseless acts of violence.
Had the film embraced its sci-fi horror roots, I think it would have played better: it was a little too grandiose, a little too ambitious for its own good. But there's still a lot to like. I found it well-cast (Guy Pierce in heavy makeup aside), and the main characters were interesting (though the film did half-ass its treatment of stock characters by giving them quasi-personalities when they would have really just been better off serving as fodder for the body-count). Fassbinder and Rapace were particularly good, and I also liked Charlize Theron in this. Visually, the film is impressive and evocative of a bygone era of sci-fi (a lot of the visual effects look like they were transplanted from earlier Scott films). The violence is for the most part unspectacular, but the self-administered c-section was fun. And the links to Alien were far more explicit than I had anticipated: the end made it VERY clear that the events of this film were formative in the genesis of the xenomorphs from the Alien films. It wasn't terribly scary though--Alien was a horror film, Aliens was an action film, and this really was neither.
So, yeah, I liked it. I didn't love it; I really wish a script that better connected the dots (perhaps in a subtle manner) had been written. Unfortunately, it comes across as both intellectually ambitious AND lazy at the same time.