My interpretation of the opening scene was that from the Engineer drinking the black goo he created all intelligent life on earth. He basically started evolution, falling into the water is why the first creature were water based, before going on land, etc, etc.
But, as I said, why are we at the "end" (or "present") of the evolutionary tree identical with the Engineer at its "start"? If he kick-started all life, starting with single-cell organisms, then it seems absurdly contrived for millions of years of evolution to result in creatures who share identical DNA with the creator of their most distant amoeba-ancestors. It would also require Engineer civilisation to have been static for all of those millions of years, since they are much the same when Shaw and co find them as they were at "our" start. Also, what about the basic plant organism that already exist on Earth when the Engineer drinks the fluid? If they are there already, then he isn't starting "all" life, and you have to stick a pin somewhere random and arbitrary in the evolutionary thread work.
My interpretation of the cave paintings was that the Engineers have visited the planet since to see how their creations have been doing, maybe stirring them in the direction they want.
I think there are two factions (at least) of Engineers. I think the monastic types we see on a primordial Earth are cultists of some type, who have rituals surrounding suicide and creation. I think there is another group who are racial purists, and that the Engineer Shaw meets is one of these, which explains why he is instantly aggressive to her and her party, and why he and his colleagues have a mission to destroy us and presumably recolonize Earth.
I think the Cultist group might have revisited Earth once humans were fully fledged. But why did they leave a star map to biological weapons base? Who knows. Maybe it used to be their Cult center, but the Racist faction found out about it and turned it into something less friendly.
Well, essentially they did create them, the black goo got into Holloway, he mated with Shaw, she gave birth to the squid thing which impregnated the Jockey, from which the proto-xenomorph sprouted. Now how it got from that state to the Alien we know is a question for the sequel.
I am not satisfied about what the squid was, how the ooze works, or why the complex sexual transaction you describe results in a Xenomorph. This can't be the origin of the Xenomoph species if it only creates one, and then by chance, anyway.
From the cave etching and the 2,000-year-old dead Engineers with burst chests, the Xenomorphs clearly existed before. The one at the end is not the first, just maybe the first one in recent history.
My impression is they created the Xenomorphs as a biological weapon but lost control and were nearly wiped out by them.
Eventually, with no new hosts/prey, the Xenomorphs died out...and now through a series of unfortunate events, have been recreated.
I think those are all pretty compelling ideas. But they are slightly weakened by the fact that serpent/squid/proto-Xenomorph physiology and reproduction is so greatly at variance with that which the Xenomorphs exhibit in other "Alien" films.
Are the Xenomorphs the bioweapon, or is it the goo? If its the goo, then what is the independent origin of the Xenos?
I was thinking the Xenomorph got made by chance with Hollway passing it to Shaw who in turn got rid of it and it got the engineer.
It's clear enough that that is how that individual Proto-Xeno was created, but it is really unclear how or why, and it doesn't seem at all possible that that individual event could form the origin of the Xeno species.
