I think it was a fun film to watch, but ultimately a giant tease and a bit of bait and switch. It's a shame that such talent came together to dicker about and not get much accomplished. The acting, especially by Fassbender and Elba, was fantastic; the art direction and photography were great; the VFX were spectacular (the 3D star map sequence with David in the alien ship nearly saved the entire movie.)
Ultimately, however, the movie threw out questions and then didn't bother to explore them or answer them. It reminded me of a brainstorming session that never coalesced into an idea. We now know that the engineers seeded Earth and other planets with human life and then developed the classic xenomorph as a biological weapon which was intended to destroy human life but ultimately destroyed its creators instead. That's cool. But we knew all that halfway through the movie. The BIG questions - Why did the engineers create us? Why did they decide to destroy us? Are they what we believe to be God? - remain frustratingly unanswered. Instead, Shaw and David's head decide to pursue those answers further, presumably in a sequel. I feel sort of swindled, as if I watched Citizen Kane and the last scene was a reporter telling another reporter, "You know, I wish I knew what Rosebud was. It's probably kind of important. Let's make an effort to find out, shall we?" and then fade to black. Perhaps those questions will be answered in a sequel, but if that's the case then this film cannot stand alone as anything but a two hour trailer. It's no surprise to find that Damon Lindelof wrote the script...he's used to teasing the answers to big questions and never delivering.
I don't have a problem with ambiguity per se, but this story builds toward a revelation that never comes. At one point I looked at my watch and realized the movie was almost over and wondered how they'd fit all that stuff into ten minutes. Of course, they didn't. I think it might have been a ballsier, more complete film if it more directly embraced the "Chariots Of The Gods" philosophy that it flirted with. The aborted plotline of Jesus as an alien, while silly on its face, would have completed the circle and made the rest fit together better.
My final complaint is that the big revelations of the movie were disclosed in hearsay dialogue but not SHOWN. The pilot tells everyone that the xenomorphs are biological weapons, but doesn't explain how he knows and nobody questions him. David tells everyone that the cave is really a ship and the room with the "vases" a cargo hold, but doesn't explain how he knows and nobody questions him.
I suppose the film's ideas have some value, because we're debating it so hotly. But maybe we're debating it mostly because it didn't make the effort to debate or examine the ideas itself.