"Alien Prequel" becomes "Prometheus".

Prometheus - The Return of the Space Jockey

The Alien Prequel's name changes to Prometheus in 2011. The idea of having a name that wasn't anything to do with Alien comes from Tom Rothman, then the 20th Century Fox CEO.

1. Variety: "Ridley Scott will direct and produce the project along with David Giler, Walter Hill and Tony Scott. Project was originally billed as an untitled "Aliens" prequel until Fox named the project "Prometheus" in January."(Variety, Feb 11th, 2011) (N.B. Although the names remain on IMDB with their respective roles in the movie, shortly afterwards Variety removed the information about David Giler, Walter Hill and Tony Scott from their own website.)
2. MTV news Interviewer: Ridley said it was your idea not to include Alien at all in the title of the film
   Tom Rothman: Yes, and it's one of the things I'm excited about, because the easy thing to have done on the movie would have just make an Alien prequel, ahm, and that's where it started as an idea, but as we talked about it the last time, it evolved, and Ridley's ideas are much bigger than that, it really is a brand new film and this is the man who made Blade Runner and he hasn't made science fiction films in 30 years, and to tell you the truth, I didn't want to undersell it, I wanted, and Prometheus is an ambitious title, I hope everybody knows, Prometheus, big ideas, it's the name of the ship in the movie, Prometheus is also the god... the titan who stole  fire from the gods, gave it to man and payed a serious price for it, so it was be careful what you're doing, so a cautionary guide, Prometheus, so it's a big bold new idea movie and I wanted a new title because, we really wanted people to know, that A, this movie stands on its own, if you're a fan of Alien, great, but if you're not, the movie's entirely self contained and full of new ideas (Tom Rothman interview with MTV News, about Prometheus Could be R Rated, Apr 26, 2012)