What did you decide about the Prometheus bio-weapon?
Potential Spoilers behind the cut...
In retrospect, I think the "Space-Jesus" theory was either an after-thought, or a red herring.
The 'engineer' who dissolved himself into the primordial soup came from a different design of star ship than the ones waiting for our expedition. Either the design and mission changed over time, or they came from a different faction, hostile to the child races.
The engineers began leaving star maps for the human race over 35 thousand years ago, to a planet that was at best a testing ground, and at worst, a death-trap. They knew very early on, that the competitive forces of evolution might produce a child race that was both very intelligent and very dangerous. It makes sense that they would want a chance to evaluate their progeny before inviting us home to dinner. On the other hand, the shrine to what we call the xenomorph, makes no sense to me. If it was indeed a weapon that the engineers developed to exterminate problem children, and they had an accident with it, they certainly didn't need a shrine to it. Perhaps the shrine was simply a first layer of trap for the not-so-terribly-bright.
Was this movie anything more that a promo for its own sequel?