Interresting prologue, with a nice atmosphere, I think.
As for the Engineers, as of now, there are multiple possibilities (I haven't read recent articles).
In an ideal world we coud have a complex scenario : multiple factions, multiple variants of the species, etc. I've a proclivity to like complexity, I admit it, because it's funnier for someone like me, and it feels more real, furthermore. ^^ But in this kind of movie, it's rare to have such a thing (I laugh everytime people say parts about politics in Star Wars I were boring - it was what, ten minutes of the film, and it was a simple matter).
The space-faring Engineers could be a tiny section of their society (the species itself can be as complex as ours) : scientists and astronauts, with a system of caste, or oligarchy, which would explain some elements, I think.