Ridley Scott on Prometheus:

“While Alien was indeed the jumping off point for this project, out of the creative process evolved a new, grand mythology and universe in which this original story takes place. The keen fan will recognize strands of Alien’s DNA, so to speak, but the ideas tackled in this film are unique, large and provocative. I couldn't be more pleased to have found the singular tale I'd been searching for, and finally return to this genre that's so close to my heart.”

So it will be in the same universe as the previous films, but will deviate from it in most other ways. Sounds better than ever if you ask me!