I liked it but the complaints are mainly:
-How did the scientists, one of whom was in charge of 3D-mapping the site/ship and had a video screen of his digital "dogs" on his suit, get lost?
He only knew where his "dogs" were. The people onboard Prometheus saw what the dogs were mapping, not him.
-Why would Holloway become bitter after only being on the moon for six hours and finding one dead alien body (which still partially proved his theory)?
Because he wanted to meet a living being he could ask questions, and then found out the only people who could answer his questions had been dead for 2,000 years.
-Why would a biologist pet a mutant snake after being scared earlier of hearing there is a life form out here.
That part was foolish on Milburn's part.
-How did the geologist come back to the ship after having acid sprayed on his face?
Because he was mutated by the black goo into a super-strength zombie?
-Why didn't David or anyone else check on the mutant baby Shaw had (I personally think there is a deleted scene that will be in the DC of David seeing it is still alive, smiling and locking it inside that room or something to that extent)?
I don't think everyone on Prometheus even knew about the baby, and those who did dismissed it becaused they thought it was dead. David was doing Weyland's bidding trying to find a key to immortality. I doubt Weyland was very interested in a dead baby squid creature. David would have been curious, but he had more pressing matters to attend to.
-Why did Shaw and Vickers feel the need to run straight from a narrow ship that was falling directly at them?
That was dumb.
-If there were more ships on the moon, why did the Engineer choose to chase and kill Shaw as opposed to just going straight to another ship and completing his mission?
Because he was pissed and wanted to kill her?
And then there are some that aren't plot holes but people were unhappy about (I not being one of them) and lump them in with other complaints.
-Why did David infect Holloway? (Because it's implied he was given those orders by Weyland and it was an experiment to do before finding an engineer. It is up to the viewer why David may have picked Holloway as it's not stated if Weyland said him or just anyone)
I don't think it's made clear Weyland ordered David to infect Holloway, although I think it was implied by the David/Vickers corridor dialogue. Maybe Weyland wanted to know what the black goo would do, and if it was some Fountain of Youth thing, so David tested it on Holloway to see what happened. David was also naturally curious himself, and may have used Holloway as a guinea pig of his own initiative. I got the impression he also got a measure of satisfaction from specifically infecting Holloway because of the way Holloway was a dick to him.
-Is Vickers a robot? (She's not. She clearly feels true resentment that her father, besides refusing to die and relinquish power to her, prefers his robot creation over her. She even has sex with Janek to prove it to him and also the audience.)
I don't think so. The whole reason for her resentment was that she's Weyland's biological child, but he shows more affection for a robot than her.
-Was that Earth at the beginning of the movie? (Yes.)
Obviously.
-What did David say to the Engineer? (It is clearly up to the audience to decide if he genuinely relayed Weyland's questions or if he said something else to provoke the reaction. Depends how you want to read both David and the Engineer species.)
No way of knowing. I suspected he might have deliberately tried to sic the Engineer on Weyland and said something like "they are here to steal your ship, I am not one of them". Can't know for sure though. If the Engineers were planning to destroy Earth 2,000 years ago, maybe he would have been hostile no matter what. He certainly jumped straight back into the game plan by trying to take his ship and the black goo to Earth.
-Did the aliens create life on Earth? (Yes.)
At least human life, I believe, is the clear implication.
-Why did they create us and why do they want to destroy us? (It's up to the viewer. There are number of credible theories that convincingly point to allusions towards Christianity as well as Sumerian creation myths or just personal readings of the Engineers. It's up to you....and/or a sequel).
Up to interpretation. Ridley Scott says Prometheus was based on Persian myths, in which case the Engineer at the beginning was a sacrifice to create humans from his remains to terraform the Earth, essentially. Some fans also theorize Christ was an emissary from the Engineers, and we angered them by killing him. That would approximately fit with the 2,000 years ago timeline. Or maybe we were just deemed a failed experiment and they were trying to "weed the garden".
There's more stuff, but I think that covers the basics.