Deck'ard nailed it.
Prometheus isn't just dumb, it's crazy, but not even in a fun way. Lindelof is a hack who does nothing but use Christian symbolism to conceal his complete lack of imagination and depth as a writer.
Having 'mysteries' that are unanswered is not the problem. It's that the mysteries are cheap bullshit, the likes of which you'd see on LOST (surprise, another thing Lindelof was a part of). It's like "omg that was weird, I wonder what that was about!" But in the end it's about nothing. That's why the movie doesn't answer it, because it can't. It's literally nothing. Cram in enough of these "mysteries" and it gives the semblance of depth, or at least some kind of grand, unifying vision behind the movie. But really, it's literally nothing.
Lindelof has figured out that if you throw in 30 or 40 asspulls in a movie, viewers can't completely keep track of them all and will just assume it all checks out somehow.