Before Damon Lindelof arrived to rewrite PROMETHEUS, the first script by Jon Spaihts originally contained a lot of ALIEN references which wouldn't surive to the completed film; in fact, Damon Lindelof felt that Spaights' script functioned as more of an ALIEN reboot/prequel which is apparently why he decided to ditch most of those ideas in his rewrite.
Damon Lindelof spoke with THR during their Hollywood Masters interview series and revealed why he felt that he had to give PROMETHEUS its own direction.
The language of Alien Zero was very much an Alien reboot, in my opinion. There were facehuggers, and xenomorphs, and eggs, in the language of that movie, by page 30. I had heard this thing was a prequel, and there’s a problem with prequels; there’s something I don’t like about prequels, which is there’s an inevitability, that you’re just connecting dots.
Prequel's are a difficult beast to tame, but they can definitely be done effectively in the right hands, unfortunately, as Lindelof says, they can just as easily feel as though they're merely connecting the dots; Damon Lindelof used the Star Wars prequels as an example:
So this idea of the Star Wars prequels, for example, is you’re going to make three movies where you basically just tell me what I already know. At least embed a new idea in there that I didn’t already know, or introduce a different thematic. Like, what if Obi-Wan Kenobi had stolen Anakin’s girlfriend away from him. And that way, when I watch Star Wars again, I’d realize, “Oh, that’s why Obi-Wan Kenobi is letting Darth Vader strike him down, ‘cause he feels guilty. That’s why Obi-Wan Kenobi is watching over Luke, the progeny of the guy that he screwed over.” So you know, embed a new idea.
Lindelof, who said that Jon Spaihts' draft contained "a lot of really great ideas", then took the core of the script and reshaped it so it could function without any of the ALIEN elements which we're already so familar with.
The opening of Prometheus as you see it was in Jon’s script. Oh this is a movie about scientists who are searching for the existence of their creators, and so there’s this kind of religious spirit, a pseudo-spiritual thing told in scientific language. And then what was really interesting to me was there was a robot along for the ride, an android, named David in Jon’s script, and I was like, “Oh this is cool. These idiot humans are basically going and looking for their creator.” And anybody who’s ever watched a science fiction movie knows, all great sci-fi is: don’t cross this line; there are questions that mankind should not answer, do not reanimate dead bodies. And it’s like, “Well let’s f—ing do it anyway,” and then it doesn’t turn out well. And because it’s an Alien movie, we know how it’s going to end.
But that was an interesting idea, because the android was there, and he’s there with his creators, and they’re seeking out their creators. And he’s not impressed by his creators. The android, he’s the smartest guy in the room, and I was like, “I’m going to take those ideas, and I’m going to say that’s what the movie is, and we don’t even get to anything, any familiar Alien language, until the end of this movie and if there was a sequel to Prometheus, it would not be Alien — it would go off in its own direction. And therefore it would be exciting to watch because we’re not just connecting dots.
Unfortunately Damon Lindelof's contributions came under fire once PROMETHEUS was released, with many critics calling the story weak and targeting the character's lack of common sense. ALIEN: PARADISE LOST, the upcoming sequel to PROMETHEUS, will still be heading in its own direction thanks to Lindelof's rewrite, although recent comments from Ridley Scott seem to indicate that it will have more of a connection to ALIEN this time around, but that we're still several sequels away from tying in with ALIEN directly.
Would PROMETHEUS have been a better film had it embraced its ALIEN roots from the start?