It was originally a prequel, then the studio brought in Lindelof to step it back.
People don't seem to understand what has occurred, this was a fully fledged Alien prequel depicting the space jockey. Aliens, face huggers, everything.
Instead what we have is something Inbetween, but it also completely destroys any chance of us getting the Alien prequel it should have been. You can be happy with whatever you got out of, cool, don't mind that, but this isn't the film it was meant to be originally, John Spaihts confirms this.
But this was a poor hash, by a poor writer. Lost went on hiatus in s03 because the Lindelof and Cruse couldn't write for toffee and were getting 'lost'. They brought in Brian K Vaughn who wrote the majority of what occurred post hiatus, story wise up to the end of s05.