Got Alien and Aliens on glorious blu ray. Amazing films. And it's funny how many influences of both films (not only in the story) can be seen in Prometheus, and yet Prometheus doesn't really seem to fit in there.
It the basic late prequel problem perhaps. Prometheus, for example, looks a lot more high tech than Nostromo or Sulaco, yet these are supposed to be almost a century after it. And then there's issues like the size of the Space Jockey (it's MUCH larger in Alien) or that the thing is "fossilized".
Unless they come up with something smart, I don't see how these films could ever be really connected.
Compared to Alien, Prometheus feels much faster, clearer, cleaner, by the numbers. It's a lot less scary and has less impact than Alien because of that.