All four films in the Alien franchise have been rated R. In the case of Scott's original film, there isn't actually that much violence, but when something bad does happen, it happens hard, with a visceral impact that, in one particular instance, became downright iconic. There was also plenty of casually crude language demonstrating the blue-collar nature of the Nostromo's crew.
But Prometheus is a very expensive movie, and economics dictate that a projects with such sizable pricetags are frequently required to be rated PG-13 so as to not limit the potential audience. Scott is aware of this, and JoBlo has transcribed his thoughts from the new Empire issue, in which he said, "The question is, do you go for the PG-13, [which] financially makes quite a difference, or do you go for what it should be, which is R? Essentially, it's kinda R... It's not just about the blood, it's about ideas that are very stressful. I'm not an idiot, but I'll do everything I can to get the most aggressive film I can."
As for just why he was compelled to return to a franchise that it's safe to say tapped out definitively around the time Fox made AVP: Alien vs. Predator. It was the Space Jockey glimpsed in Alien, he said, explaining, "I always wondered when they did [Aliens] 2,3 and 4 why they hadn't touched upon that, instead of evolving into some other fantastic story. They missed the biggest question of them all: who's the big guy? And where were they going? And with what? Why that cargo? There's all kinds of questions."
Prometheus started out a script by Jon Spaihts, then Lost executive producer and Star Trek 2 co-writer Damon Lindelof was brought aboard to revise the screenplay. Saying the words in that screenplay are actors Noomi Rapace, Idris Elba, Charlize Theron, Michael Fassbender, Sean Harris, Rafe Spall, Guy Pearce, Kate Dickie, and Patrick Wilson.
Procure your Rogue 3D Eyewear before Prometheus, Scott's first 3D venture, arrives in theaters on June 8th.