I love it to...it's the best kind of sci fi. The script definitely benefited from having some writers from Lost. I'm thinking we may even have to come to terms with the idea that we may never even know how the original derelict craft got there in the first Alien, even in the sequels. Not answering that but still addressing the space jockeys keeps the mystery of the first Alien alive while still giving us sci fi nerds something to obsess over. This was actually something I was worried about with Prometheus - as much as I want those questions answered, part of what made the first Alien so great was the mystery. Specifically revealing what happened would kill some of the mystique.
What I'm starting to think is that the goop when spliced with DNA from another organism ALWAYS results in some form of xenomorph. That's why it still takes on some characteristics of the host...it utilized its DNA to make itself all over again. This is why it was a dog type alien in Alien 3 since it used a dog as a host. The organism is a survivor that always manages to recreate itself. Impregnating Shaw and splicing with one of her eggs directly allowed her to produce another facehugger while not killing her. When combined with the DNA in a non-reproductive capacity, it simply kills.
There are a lot of unanswered questions about this as well...did David know about this? He was experimenting quite a bit and surely he is incredibly smart (being an android). He had to of picked Charlie to infect because he knew he and Shaw were intimate. On that note, I also feel he told the engineer in the end to kill Weyland (or that the group was there to harm him). He did mention earlier that he felt all children must want the deaths of their parents.
I'm starting to go off again on this...but just a couple more things I thought of. Vickers had to be an android. She called Weyland "father" and he had mentioned he never had any kids...David was the closest he had. We also never saw any blood when she died...and her death was very quick. We also never saw her wake up from hypersleep with the crew. That might come back later.
Similarly, Weyland will have to come back in some capacity. Why else would they bother dressing up Guy Pierce in old guy makeup when they could of just found a real old guy. Something's up there.
On that note, at the very end of the credits there is a logo for Weyland and the date 10-11-12. Check out the website
What Is 10.11.12? ...it's got some cool stuff. More questions than anything, but it's worth looking into.