As vague as Prometheus was at times, I thought it did a really god job of feeling like a part of Alien, even though there weren't any Xenomorphs. I also thought the final version was much better than the Spaihts script. I think the biggest similarity to Alien was that there was in fact a lot of mystery, and things left unexplained. As much as I love the other Alien movies and stories, the lifespan and nature of the standard Xeno has become too predictable and familiar. Even though it would have been nice to see the Xeno in Prometheus, it's better to have little to no information than know everything. I think it was Dan O'Bannon who stated something along the lines of as soon as something becomes familiar it's not scary anymore (it may not have been him that said that, but I think that's right), which has indeed happened to the Alien universe. I also think it was important for them to do something more than just provide some new monsters. Those creatures did seem cool, but the monster has never been the main thing that makes the Alien films truly scary or mysterious. It's always been about the atmosphere of the films, and the overall sense of dread or impending doom, which Prometheus nailed.