Although I enjoyed it immensely at the time, having now had more time to think about it, I agree with Joramun's true spoiler. Much of the film simply does not make sense, and there are far too many times where suspending our disbelief is very difficult...
Elizabeth Shaw running around quite happily after giving herself a caesarian was especially daft, regardless of how many drugs she'd shot herself up with.
I think the overall story is actually quite a good one, it just wasn't executed as well as it might have been.
While the idea that mankind is an evolution of a space faring race is not a new one
, I thought the way it was done here was OK. I was a little disappointed though that
the Engineers were actually human looking underneath their bio-mechanical armour, I would have preferred somehting truly alien -- but then again, it's hard for us to relate to things that are totally alien, so in some ways this was the most obvious thing to do, and it was obviously a major plot device anyway.
.
The
black liquid dna mutator/evolver
was a good plot device, and I think it was very clear throughout the film that it had
multiple and awesome capabilities
, so I'm pretty happy with
the 'birth' at the end of the film
being part of that plot. Of course, it makes no sense at all that
the critter Shaw removed from herself grew into that massive tentacled proto-facehugger with no source of food, but hey...
As for how that relates to the future alien lifecycle seen in the films we already know -- well, you can assume that the first alien continued to mutate and evolve and created a new lifecycle after the events of Prometheus. Unless of course
that wasn't the 'first' alien to ever evolve, but was in fact the intended result of the Engineer's mutator; after all, the mural seen in that cave with the big head clearly has an alien in the middle.
I was a bit annoyed by a lot of the contrivances used to get the plot to go where it had to go.
Helmet removal, playing with mutant worms, etc
. Trained scientists just wouldn't do stuff like that. But heigh ho, it made for some interesting and fun scenes!

I loved the
holographic recording of the Engineers trying to escape at the beginning of the film, and then finding the piles of dessicated bodies
, that was all suitably eerie and tied in well to the vibe of the original Alien film.
I could list a lot of other issues, but I would be a bit churlish since despite all the issues, I actually really enjoyed it. The 3D was very good too, although I watched it with those really slim Dolby 3D glasses which didn't fit properly over my own specs, so it didn't completely work... and some scenes where the focal point changed rapidly were very hard to watch in 3D.