The main things I was wondering about: just what is that black goo? Does it have a specific purpose/function? And what are the motivations of the Engineers (in particular, why is the one that's still alive such a violent, aggressive asshole)?
I'm glad someone else is wondering about that besides me. It seems to cause heads to explode, turn people into zombies, and also cause them to have crazy mutated babies. It's a multipurpose goo.
it also seems to have given rise to the entire human race (or was that a different kind of goo?)
It also seems likely that it mutated the worms that were in the room with the head statue to turn into the snake creatures.
I am also wondering what the purpose of that room was. If it was a storage facility for the bottles of goo, why was there so much more on the ship? And why were they activated by opening the door? And why we're all the dead aliens trying to get into that room? And why was the big head there? And why did the mural on the ceiling change after thy entered the room?
And the biggest question: why were all the ancient pictures On Earth directing them to that planet?