These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Alternative Character Interpretation: David and exactly how much emotion and free will he really has. Fan opinions seems to range from him being entirely emotionless and simply following Weyland's orders to being entirely sentient and deliberately seeking out loopholes in his programming. Sound familiar?
Did he infect Holloway because Holloway was the most convenient target, or because he was the human who had been the biggest jerk to David?
Awesome Music: If there was ever a piece of music that perfectly represents the sheer awe and majesty of creation, then, "Life" is it. "Earth" could count as well.
Big Lipped Alligator Moment: The coda showing the birth of a "proto"-xenomorph, a scene created to connect the film to the greater Alien mythology. However, audiences new to the context of the film don't know what the point of this critter is, since it was never foreshadowed, and it has no impact on the narrative, characterization, or the central conflict of the film, and have therefore found the epilogue confusing and out of nowhere. Audiences who know about Alien will acknowledge the connection, but since the action for a potential sequel has now moved offworld (with Shaw and David traveling to the Engineer planet) and Prometheus takes place on a wholly different planet from Alien, the scene is a narrative dead-end.
Critical Dissonance: While certainly not perfect, this movie scored a respectable 73% ("Certified Fresh") critical rating on Rotten Tomatoes—far higher than Alien³, Alien: Resurrection or either of the two Alien vs. Predator movies—and its audience rating was almost as high. Still, to hear some longtime Alien fans talk about it, you'd think this film was a complete disgrace to the franchise with no redeeming qualities whatsoever.
Not the film itself, but in real life, a Moral Guardian ticket vendor tried to push away people from the film by claiming that Shaw self-performs an abortion. The procedure in the film was not an abortion but a c-section. If it were an abortion, the fetus would have been killed, which it clearly wasn't. Also, perhaps most importantly, it was an alien-squid-abomination that would no doubt have ripped its way out of her given a moment more.
Freud Was Right: Where do we even start? Parent/child issues (both literal and metaphorical), pregnancy-based Body Horror, an android who may or may not have the hots for the protagonist, rape themes, all kinds of disgusting organic things being inserted in bodies. And of course, many, many things shaped like dicks.note Par for the course for both Ridley Scott and the Alien franchise.
The crewmen who have a running bet with each other throughout the movie, Ravel and Chance. While they are more likely just friends or at least on familiar terms with one another, the duo did have an awful lot of significant glances and nearly all of their screen time was with the other.
Also Millburn toward Fifield. He seems to be laughing at his comment early in the film in a way to gain his approval.
While the movie is a visually and aesthetically amazing piece, the plot and behavior of the crew is a mess. Just look at the Idiot Ball section to get an idea. Honest Trailers described the crew like this:
It's the Same, Now It Sucks: A major weakness of Prometheus is how similiar it is to Alien. In particular, Alien was revolutionary for having its protagonists be Space Truckers, but here, when the characters are scientists who should be highly motivated about the subject of their research, why are they still acting like Space Truckers?
Love It or Hate It: If you believe the internet, this movie is either a misunderstood masterpiece or a total disaster.
One-Scene Wonder: A proto-xenomorph shows up only for the last minute of the film, and was a huge hit with the fanbase.
Paranoia Fuel: David can access the memories of the crew whilst they are in stasis. They've been in stasis for over two years. Furthermore entrusting your life to an amoral synthetic for that length of time is unnerving.
Special Effects Failure: In a film that is by and large astonishing to look at, Guy Pearce's terrible aged make-up really stands out, the result of prepping a design on the fly during a then-tighter schedule. One could explain it in-universe as side-effects of Weyland trying to extend his age, but it can still be jarring.
Spiritual Antithesis: It actually has some elements of this with Aliens. Where the movie Aliens uses the xenomorphs as metaphors for the pains of childbirth and parenthood, the aliens in Prometheus are used more as metaphors for hostile, overbearing parents.
Squick: A completely uncensored emergency c-section, anyone?
Visual Effects of Awesome: Save for Guy Pearce's faulty makeup, even those with a negative opinion on the film can agree that it looks incredible, especially in 3D. Some examples include but not limited to would be the opening shots of the waterfall and the world, The Engineer's sacrifice, and the Starmap.