Judd, I think it would be really cool if in "Paradise" Shaw and David find out the "real" aliens are the xenomorphs and that the Engineers were "robots", or genetic machines if you will, created by the xenomorphs, which will show how technology can get so streamlined with genetics and everything that it's hard to tell what is manufactured and what is a living being. I don't know if this is one of the wacky ideas being tossed around, but I guess I really want the xenomorphs to be the real aliens because the Engineers looked like WWF wrestlers.
Are the xenomorphs really that intelligent? I find it hard to imagine the prototypical Alien with his fangs and claws, looking through microscopes and holding delicate beakers! They just don't seem like they have the patience if you will. But it's pretty clear from Prometheus that the whole life generating and changing "goo" found in the vases became
the xenomorphs (through the help of both human pregnancy and the engineer as the hosts), at least the one at the end of the movie. Maybe if your scenario were true the original xenomorphs have far greater intelligence and are more evolved, wherein the aliens we are familiar with are just combinations of genetic breeding. Not sure I'd be satisfied with that direction, but there is definitely the question of where the engineers came from and how exactly they were able to engineer anything (the best sci-fi explanation), if they decide to answer that at all.
Too bad that link went down, I watched it once more and thinking later, I may have caught a movie mistake:
Remember when Shaw stumbles into Weyland's room after the surgery? There are numerous people surrounding him, including David and the "bodyguard" guy who ends up dying by the hands of the Engineer in the bridge. I seem to remember a few extra people in that room- there were 2 very identical looking guys standing guard right at the door. Is it me or were they completely unaccounted for later- happened to them? Only people who died in the bridge of the Engineer ship were Weyland, the "bodyguard", the woman with the thick Scottish accent... anyone else? It seemed some of Weyland's attendants were completely cut out and forgotten about- wouldn't they have come to the bridge of the Prometheus ship as it was taking off without Weyland (and about to go head-first into the other ship)?
Maybe they were in the rover waiting outside the big dome while all that was going down and never had time to make it back...