Great excerpt from a Lindelof Interview from last year. Basically sums it up.
Its amazing how many people had a hard time with this film. Its like they couldn't grasp it and just are not open to some things being a mystery. Its like movie goers now need everything spelled out.
To me how I felt all along is Shaw was our eyes, and we only know what Shaw knows. And now she's off on to further her quest and hopefully we will see her again.
And yes the movie definitely was connected to the Alien movies. Its just a different part of the story. Its not Ripley story here, its Shaws/Weylands for the most part.
"I don't want to talk too specifically about what the black goop does. Obviously the characters in the movie are trying to theorize based on what is happening to them. "This thing is a weapon, it's really bad for us." When it interacts with living species, bad things result. So you see little worms and when the black goop gets on the little worms we see what happens to them. And when Fifield gets it all over his face mask, we see what happens to him. When Holloway just has a drop of it in a glass of champagne, we see what happens to him.
We wanted to be purposefully vague, [but steer] the audience towards some conclusions as to what that stuff was supposed to do: Is it supposed to kill you? Is it supposed to transform you—which seems like the most obvious choice—and to what end? Like, why in God's name would the engineers want to create abominations out of mankind? Some of these questions we wanted to answer directly and some of these questions we didn't want to answer directly, which sets you up for a certain level of frustration and disappointment that I am well familiar with, but I'll take it any day of the week because I also feel like it forces you to fire your own imagination.
We clearly have answers for those questions ourselves that we did not present in the movie purposefully, not just because we're saving them for potential sequels, but because the power of the original Alien—or even Blade Runner—is that to a certain degree, we're giving you all the numbers in the equation but we're not adding them up for you. And that's intentional."
ok done.