There are now two movies in the Alien sequence.
Let me clarify this a little. There's a difference between what happens in a story and what it's actually about. In 1979, Ridley Scott's Alien was released, and it told the story about a motley crew that ran across the wreckage of a ship with the corpse of a giant. Of course, eventually that crew is terrorized and eliminated, one by one, by a vicious alien, and the only survivor is Ellen Ripley.
Subsequent movies inspired by Alien involved both the alien and Ripley, and they were of varying degrees of quality, but it wasn't until Ridley Scott himself returned to the franchise that the story from the first film continued. So now we have Prometheus, the origin of that crashed ship, and what it's all about. Yeah, so the answer is, not that rampaging alien, and not even Ellen Ripley. It's about the quest for knowledge, about selfish and self-destructive desires, about the nature of intelligence, about endurance, about self-preservation...Basically it's about everything but everything Alien actually inspired.
Prometheus is almost exactly like all the other movies in the franchise, and yet it's the first one since the first one to actually be relevant, to try and continue the greater story. We discover what exactly that alien was, how it came into being, and maybe that answers some of the questions that movie itself poses, about the burning desire to know where mankind came from and why it came into being. There's a lot to do with science but very little actual science going on. It's a parade of human foibles, even from the android who's the most manipulative one of the bunch, worse than the old man and his young daughter who attempt to dominate the conversation but have nothing to say, or the two lovers who never stop to think about consequences, or the impulsive rebel who doesn't want any trouble but keeps walking into it, or the pilot who knows better than anyone when to walk away but can't bring himself to do it before it's too late. Did that first Engineer we see get exiled and poisoned, or was it deliberate?
I'm not much for horror, and horror can be more horrifying in an age that can show unnatural things acting naturally, so clearly that was not my interest in seeing Prometheus. I'm a bigger fan of Ridley Scott than Alien, mostly because Alien was always buried in a franchise critics grew tired of without realizing why, but now I think I may understand more of it than before. Scott is a man who brings his particular vision to all of his projects, and he doesn't usually go back to a subject once he's covered it. When he does it's because there's more to say, not more to see. He's one of our most cerebral filmmakers, so of course he's rarely among the most popular. Prometheus is the first time he's been culturally relevant since Gladiator, and that was more than a decade ago. We happen to be in the thick of a period where someone like Christopher Nolan can be wildly popular. That's why something like Prometheus can happen. The whole reason that game of whether or not it was related to Alien was necessary because it forced fans to wonder whether or not it mattered that those aliens or Ripley were present. Once you eliminate them from the equation, then you have possibilities again.
When people wonder whether Hollywood is creatively bankrupt, they look at the summer blockbuster schedule and count the number of sequels. Well, Prometheus is a sequel. And it blows all those assumptions out of the water.