The list of nonsensical plot points and dead ends Nicole and I came up with as were driving home from watching Prometheus kept us talking the entire way. And yet I can't say I didn't enjoy it. That being said, I need to vent. Spoilers aplenty up ahead, to read at your own risk.
1: What was the big damn deal about finding the cave painting in the opening when only a few minutes later into the film they reveal that there are many of these?
2: Why does Weyland hide his presence on the ship? The guy is a billionaire and has the hubris to, you know, ask "god" for eternal life. I doubt he cares what anyone thinks of his accompanying the mission. The two people effectively at the head of the expedition are doing so because they want to say "hi" to the people who made them,, so is Peter. So what's the big damn deal?
3: What is the point of David infecting Holloway? He has no reason to believe that doing so would further any of Peter's goals. If anything, they might hamper them since Peter Weyland supposedly hand picked many of the people on the mission. You could argue that David resents his maker and he does this to sabotage things, but that doesn't hold up when you consider that he doesn't do anything to the rest of the ship, or the crew, or any of a hundred other things he could be doing to actually sabotage this event if he wants to.
4: The biologist and geologist. One second they're freaked out at being stuck in the alien facility. The next, they're goofily dicking around with dick cobras. How does Mr. biologist not recognize the dick cobra's threat display? And before you go saying things like "Well, it's not like he could know what that hissing and flaring hood meant" well, what did you think it meant?
5: Shaw wakes up from being drugged, knocks two people out, runs to the surgery vending machine and gets the horrific alien squid thing out of her. How does nobody find her in the middle of all of this? It's not exactly a huge ship. And why does nobody care that there's an alien squid thingy on the ship now?
Funnily enough I actually enjoyed this. The visuals are good, and it makes you feel small and insignificant. I'd say it was successful tone-wise if very sketchy in the character and script departments.