First off - I think the film's great. Great spectacle, great performances and interesting concepts which tie nicely in to Alien: Resurrection oddly enough.

But what I really want do do I write down my theories about what I think the Engineers' plan was, just to get it out there.

They want to kill the baby Jesus. Or rather God.

The movie establishes through the android David the desire of the creation to supersede then ultimately replace the creator just as every child does with their parents as exemplified in Vickers' (Theron) relationship with her father. It's a story straight from greek mythology of the Gods deposing the Titans and then Man battling the Gods by, amongst other things, stealing the power of fire from them.
It is the human's goal in the movie to meet their creators, but when the turn out to be a bunch of dicks they turn to killing the one they have then ultimately hunting the others down.

So how are the Engineers going to kill God, their Creator? With Alien soup. They create a bio weapon, the ultimate manifestation of which is our old friend the Xenomorph but in it's initial state is black ooze, thousands of canisters of which the Engineers planned to ship back to Earth were it not for the weapon turning on them and wiping most of them out. Noomi Rapace's character Shaw even asks what mankind had done to deserve this fate but doesn't get an answer. I think the clues are there however. David says that the Engineer has been in stasis for 2000 yeas, give or take. Well what happened 2000 years earlier , give or take, that they could have used there bio-weapon on? Well I think they were planning to kill the manifestation of God on Earth in the form of Jesus Christ, someone that is repeatedly referred to with Shaw's crucifix.

It could be possible that the Engineers deliberately seeded our planet with life to bring about this manifestation, a systemic anomaly you could call it, one that they had predicted all along. But their own creation turned on them before they could do the same to theirs.

Well there you go. Just needed to get that out of my head really, none of my friends have seen the movie yet so I needed someone to tell it to. Quite possibly a load of bullshit fanfic, but I think it holds water and is consistent with the themes in the script.

PS: Makes me look forward to the proposed Hyperion film adaptation which covers similar ground.