Oh dear - what a mess.
I'll just stick to the biology as it would take too long to try and comprehend all the other nonsensical scenes. I'm also avoided the quagmire that is the alien black oil evolution too as it makes my head hurt even writing about it.
It doesn't help that the film is convoluted making it hard to know WTF is going on half the time anyhow but at some point the "engineers" disintegrated and seeded life on our planet. Fair enough but how comes humans match the DNA of the engineers 100%? We don't look that much like them but maybe if we grew up on their planet, eating their food we would? That's not really the point though - it's more a case of how over 3 billion years of evolution has randomly wound up producing a human exactly the same as the beings that seeded our planet. Those odds are fairly staggering. Maybe the engineers kept coming back and tinkering with us but it would suggest that the engineers themselves haven't changed in 3 billion years. Is our DNA really as good as it gets? I resent having to come up with justifications for a screenplay that clearly couldn't be arsed and hoped fans would retroactively fill the gaps.
If you can look past all the biology nonsense and WTF? plotting the film is gorgeous eye candy and has several good horror moments in it.
Ridley Scott is a gifted director but he clearly can't tell a great screenplay "Alien" from an awful one "Prometheus". I think he should leave Blade Runner sequels well alone unless there is someone who has a clue working with him.