It's funny, but if you go back and read the various interviews he gave prior to the announcement, you could see the direction this was headed. He stated from early on that he felt the creature had lost a bit of mystique and the AvP stuff had further demystified it (I'm obviously paraphrasing of course). he was more interested in revisitng the concept or looking at a possible earlier original version that led up to what we initially saw. Gradually, the conversations led from the creature itself, to talk of space jockeys (which he seemed really interested in), time dialation and terraforming. You could see the evolution of ideas away from a strictly Alien movie, to exploring other concepts within that same universe.
I'm willing to bet that's what happened. The more creative minds you bring in, the more you're able to collaborate and expand upon those unseen elements to the story. Of course, what happens to your Alien Prequel when there's no Alien? It becomes something else. All of the structures still exist (Thus the Alien DNA that's so cryptically spoken of), however, you're free from the constraints of a previously established franchise, and the context that has already been explored in 6 movies involving the creature.
Honestly, I'm excited to see something original. I'd rather break the mold and move in a new direction rather than rehash what's already been done. Time for something fresh, that still at least ties into what we seen.
