Fassbender's performances were memorable, but the plot was sloppy - almost nothing about it made any sense.
SPOILERS FOLLOW:
1. They provide no explanation as to why they failed to detect this life-bearing planet.
2. As unlikely as it would be for the planet to have the same gravity and breathable air, they have no information as to the ecology, yet they jump out of their drop ship without any hazmat suits - sure enough within minutes several crew members inhale a lethal substance. That's a really dumb way to go.
3. When they inhale the substance, it causes neomorphs to pop out - within the space of something like a few minutes. If something could grow that fast, what raw materials would it be harvesting in order to gain mass that quickly? Is it sucking the dirt through its feet?
4. Later on, the black substance is shown wiping out the indigenous population like its a poison cloud. Their undisturbed remains look untouched ten years later. More importantly though, the same black substance which creates the neomorphs in humans inexplicably kills the indigenous people outright. Also, was there only one colony of indigenous people? What happened to the rest of them? Why does the flora look like its from Earth?
5. The neomorphs don't have eyes but the bright light of a flare scares them away.
6. David's a head when we leave him in Prometheus but his whole body is repaired by the time he reaches the planet - this is explained by one line of dialogue. How did David get fixed if him and Shaw were stuck on that ship? He wasn't exactly easy to make.
7. The face huggers are an inefficient delivery system for the xenomorphs, even if they can grow ridiculously fast. If it's supposed to be some kind of superweapon its one for one spawning cycle doesn't work very well. With such tiny limbs they wouldn't be able to move very far very fast, so they would have trouble spreading. Once again, a mask could easily prevent it from latching on to a host. On top of that, once born, the alien then goes around killing off all other potential hosts as quickly as possible. The spores work better than the face huggers, and they don't work too well either.
8. In other films, the queen laid the eggs. There doesn't appear to be any queens. Shouldn't that have been the first thing David designed?
9. If David designed the Xenomorphs, what are they doing on an engineers ship in the first movie?
10. If Billy Crudup didn't trust David, why did he stick his head in an egg? Why didn't he get backup?
11. Why did the guns look like something from our time? Aren't there more advanced technologies, or at least guns that don't look like 150 year old relics? We have more advanced weaponry now than what they were packing. Also, a gun would only work in an oxygenated environment, so it would be useless in most environments in space.
12. If Walter had updates, why wasn't he able to beat David?
13. If David has stolen away on board, why does he help the crew kill the Xenomorph?
I'm probably missing some stuff. But not as much as this movie.