There's a lot of stuff you just have to sort of handwave away as being either wrong or heavily under-explained to the point of being inexplicable. The Engineer dissolving into primordial ooze at the beginning to seed life on Earth... fine, whatever. Remember that these Engineers were on Earth around 3000 BCE (either returning, or having never left) to inspire our ancestors to make cave paintings and pictographs of them pointing at a specific star system. Why they created us at the beginning of the movie, wanted us dead by the end of the movie but somewhere in the middle showed up on Earth to hand out star maps to our ancestors, to point them to the planet where we could go to get killed/horror raped is... baffling. Whatever, move on.
I'm convinced the "straight lines" that Charlie Holloway saw were
nazca lines. His remark was still stupid, but having Nazca lines on an actual alien runway is a very nice touch given the aliens in question both created us and visited our descendants around the time of Gilgamesh.
I don't understand the black goop. At first I thought it was mutagen. The first room with all the containers in it had what looked like mealworms in the soil (you see them when David first enters the chamber). Goop oozes out, mealworms get mutated and you get lamprey face huggers there to throat-rape the stupid, stupid biologist who insists on petting them. However, when David puts a drop of the ooze in Charlie's drink, he starts filling up with, and being dissolved by, horror lampreys. When he looks in the mirror, he sees a little tentacle whip out of his eye. When he fucks Shaw, she gives birth to a squid. Therefore, ooze == horror eels, apparently. Why that specifically, I don't know, but then that's no more arbitrary than the original face huggers being spider-like.
The purpose of the biological weapon that is the ooze seems to be to unleash a horrible, invasive species that treats everything around it like parasitic wasps treat caterpillars, and evolves forms based on those hosts to better... well, we're not really sure why their morphology changes based on their host. Either it's to make them more effective weapons while taking down a population, or the freaky xenomorph IS the desired end-product and you want it to go all zerg on its surroundings, evolving into a superior form by modeling itself after its hosts. Having the Engineers go around seeding planets with humans, because humans are the preferred host for xenomorphs, and the xenomorphs are the desired end goal of the Engineers bio-tampering would be kinda cool. I'm not sure if the films bear that out; I'm pretty sure the xenomorphs are just there to flip out and kill stuff as horrifically as possible.
I really, really, really don't get why all the people who aren't David started acting really inconsistent, and stupid, once the storm hit. One of the two cowards decides to go all Crocodile Hunter and pet the angry alien lamprey. When folks found the engineer corpse they should have broke down and wept and thrashed and screamed and danced like they had just found the most amazing thing ever in the history of human civilization because THEY HAD JUST FOUND THE MOST AMAZING THING EVER IN THE HISTORY OF HUMAN CIVILIZATION. They even acknowledge that in their weird, wooden fashion later on. Once people started dying they should have done what the folks in
Alien did and pull back to the ship, lock the doors and start asking questions while poking samples of alien goo in laboratories. The guy who got face-raped by an alien worm should have showed up later as a mutant rage zombie, not the guy who got his face ruined by acid. And why did anyone show up as a mutant rage zombie? Infection = alien popping out = people dying, not Infection = human raging out = people dying. What the fuck was that!?
Why was the Engineer captain unable or unwilling to fly off to Earth before David showed up to push buttons? They said that the decapitated Engineer had been dead for about 2000 years so there was plenty of time for the ship to say "the last face hugger starved 200 years ago, wake up the captain so he can fly to Earth". And why did the Engineers on Earth back in 3000 BCE pointing us at that planet anyway? They were essentially saying, "Hey humanity. Once you learn interstellar travel, please report to this planet so we can exterminate you and/or use you as the fleshy test tubes for our xenomorph creations." For a species that can just terraform planets and create life, there must be more direct ways to create hosts/murder victims.
Shaw, upon finding out she had an alien murder baby in her womb, acted in a sufficiently empowered way and had the robo-surgeon give her the abortion she damn well wanted. Afterwards she... just sort of decided to tag along with the decrepit, god-complex CEO and the Aryan robot who tried to deny her her caesarian. I get that almost everyone else went stupid after the shit hit the fan, but Shaw was supposed to be the competent non-android in the mix. Sigh...
I'm thinking that the blond boss lady was the CEO's clone, or something along those lines. That CEO was waaaaay too old to have a natural born daughter that young. She might have been an android (again, the writers had a major hard-on for Blade Runner), with David being Star Trek's Data and boss lady being Data's brother with an emotion chip. Her being an android would be really stupid given the surrounding evidence, but I wouldn't put it past these writers to try and shoehorn that in.
There's more but that's enough for one screed.