And beyond that, the plot winds up being just a disjointed series of scary situations with no rhyme or reason, from the deadly black goo that is never explained to the ship's android randomly turning evil, just because.
But maybe the weirdest thing of all is that clearly the film is intended to be an Alien prequel -- the finale of the movie literally leads up to the plot of Alien. A horseshoe-shaped ship crashes with an alien sitting in the cockpit, landing in the exact same position as it is discovered by the crew in the first Alien film. "But wait," they say, "this isn't the planet they landed on in Alien known as LV-426. This is LV-223, a completely different planet. It just so happens that this planet has an identical bit of wreckage and a nearly identical species of alien on it. Makes perfect sense, really." It would be like if, at the end of Revenge of the Sith, it turned out that Anakin had actually been turning into a completely different guy who was also named Darth Vader in a neighboring galaxy.
Actually, that might be a best case scenario.
The Awesome Movie We Missed Out On:
Prometheus was just one or two rewrites away from greatness -- but not in the direction you think. An earlier draft by John Spaihts called Alien: Engineers was in fact a straight Alien prequel that, yes, took place on the same planet and could easily have been one of the best movies in the series (or at least something that wouldn't have made audiences want to reach into the screen, grab each character by the shoulders, and violently shake them until they stopped being stupid).
20th Century Fox
Where's Michael Biehn when you really need him?