Haven't seen Prometheus, but having gone through the frustration of Lost, I think it's clear that Lindelof is a hack. Are movies generally better when they clearly leave you with a definite "idea" in your mind? Of course not, but that doesn't mean that you can leave things unanswered or unexplained just for the sake of doing so. By embracing plot holes and even forgetting about entire plotlines (I'm talking about Lost here) Lindelof believes he is leaving things open ended for the audience to impose their own beliefs, imagination, or whatever. In reality, he's just being lazy.
I think a good example of how to correctly leave things open/unexplained is the sadly poorly received second X-Files movie. The question is raised throughout the film of the possibility of a divine power, but it never forces a certain perspective on the audience, trusting them enough to come to their own conclusion whatever that might be. Lindelof is not doing anything approaching this. On the flip side, given the X-Files example, I think it's fair to once again criticize the final scenes from The Tree of Life. That film would have been so much more powerful if it hadn't rammed the idea that Heaven is definite down our throats right at the very end.
A good point, poorly made?