Goo is the Egg

Looking at the black "goo" from Prometheus and the egg from ALIEN I believe we can consider the relationship is there between the two.  They are quite similar in luminescence and color.  I believe that David has been on "Paradise" trying to create life and the facehugger is what his experiments produce.  I am sure he used Dr. Shaw in these experiments, since she was, however, the first to give birth to a facehugger anyway.   She is most likely the "queen" to the xenomorph race.  I believe his attempts to use the "Engineers" as hosts has failed, which is why they are all dead.

I believe that there was a race far superior to the "Engineers" that had already created this bio-weaponry that the engineers tried to reproduce.  Hence the ancient and much larger Space Jockey in ALIEN.  "It got out.  It turned on them.  The end."

I believe the "engineers" are a race that live below ground.  Hence their whiter than white skin and dark eyes.  Their caves are where the eggs are first created and that is why the original Space Jockey ship, which looks to be crashed, is actually ready to launch from it's origin.  The creator was attacked before liftoff and therefore was unable to detach from the cave below.

The acid hole in the floor of the Space Jockey ship was an accident created from the chest burster that tried to chew it's way through the tough skin and suit of Jockey.  It was able to get out of the body but died immediately from injury.

So in essence Jockey was the engineer of the engineers.  And David discovered all their specimens and experiments upon arrival to Paradise.  And re-created the eggs that were supposedly extinct long ago.