Here's a question. Is the lack of character development for the human characters (David is the only character that learns and wonders) bad writing or is it intentional? The humans move through this alien environment looking around, hoping to find something definitive about their origins. But they don't find it immediately, only DNA samples. However interesting that may be, they do very little analyzing of what it might mean. Nor do they speculate on other things they witnessed. The two main scientists see these Engineers as Gods... and wish nothing more to meet them. Same as Weyland. Yet almost everyone in the film recklessly, hopelessly, meets some sort of end. Most deaths being undignified and meaningless. Before they realized the Engineers wish to terminate Earth/humanity, the Engineers are Gods. They have the answers. When Shaw and others come to understand the Engineers plans, they no longer hold any respect towards it. They assume its motivation and reasoning is wrong. They assume the moral ground even though that ground was built on the shoulders of the Engineers (scene with ground breaking open represents human reality/culture literally breaking open). David on the other hand, knows everything all along I think. He knows waking up the Engineers will lead to events that end humanity. His view on humanity is that if their creators saw no more purpose with humans and humans see no purpose in life then the reasons why (for any of it, origin, why we were made etc) are meaningless. The audience isn't meant to find definitive meaning. It's almost essentially trolling those who take the film seriously. Who think there might actually be some kind of answer. There isn't one is the fact. But for some of us, we can look at life around us and wonder regardless. David has more love and passion for life than humans because he doesn't pretend that his creator cares about him. He doesn't pretend that he will go to heaven when he dies. He doesn't blink an eye when his creator says he has no soul. Perhaps that is what the Engineers would have told us... but unlike David, we continue pretending, denying, and ultimately living in fear.
So yeah, I think you are right atop. This film will be looked back on more highly. At least it continues to grow on me and I still have only seen it once. It's becoming something rather brilliant actually.