Even before the Alien prequel was announced, I always imagined that it should have little to do with the exisitng movies. It should feature the Space Jockeys, absolutley. But the Aliens, specifically their life cycle, should not be revealed as it would diminsh the effect of ALIEN. Always been in favour of various other Giger inspired nasties though.
Perhaps what we're looking at here is a case of what happened with Batman Begins
. In that film Liam Neeson plays Ra's Al Ghul. However, the audience wasn't supposed to know that. We were supposed to believe he was Henri Ducard and then it would be revealed at the end.
Perhaps here we will get something similar. The film is Prometheus
, and it is about the Space Jockeys. As the film goes on, we start to think, "hmm, are the Aliens actually in this film?" because we will be led to believe they won't be. And then, sometime before the film ends (maybe even half way through, I dunno) Aliens do arrive in the film.