Space Jockey Couldn't have Engineered the Alien
Having recently watch Prometheus I was left extremely unsatisfied with the Alien's origins as it felt contrived and didn't seem to fit with what the original Alien movie subtly suggests.
Before even watching Prometheus it was pretty obvious from Alien that the Xemomorph, Derelict Space Vessel and Space Jockey were all created from the same bio-mechanical technology. For example the black bone/tube exterior and interior of the Derelict looks identical to the design of the Xemomorph, almost as if the Alien could have grown from the ship.
Then there's the Space Jockey which has literally grown out of the chair, thus the Derelict and Space Jockey are one and the same rather than whats depicted in Prometheus. In my mind I had assumed that the Derelict space vessel was completely biological which offers many advantages over metals such as titanium etc in that it can heal itself if it becomes damaged and constantly rejuvenates itself. The Derelict ship and Space Jockey were therefore engineered as one entity and acted as one life form. Its pretty obvious that the Space Jockey could not have evolved naturally based on the fact it grew out of the ship's pilot chair and is congealed both body and mind into the ship. Therefore it seems unlikely this life form was the ultimate creator of the Derelict or Xemomorph's, rather some other god like genetic engineers must must have genetically engineered these lifeforms millions of years ago. Alternatively perhaps the Space Jockey is the ultimate creator but what we see in the movie is one of result of them genetically modifying themselves to become part of their mechanical technology, i.e. like us integrating human DNA into a car or aeroplane.
Another thing again which seemed pretty obvious was that the Derelict was some kind of vessel that served a military purpose in that it was carrying the Alien eggs as cargo held in stasis under the blue mist (Perhaps the Derelict was the factory for these eggs rather than just the transport). It also looks like the Space Jockey is mounted into a large gun emplacement which perhaps fires out of the top of the ship much like a ball current gunner on an american world war 2 bomber. The base of the Space Jockey chair looks like it can swivel 360 degrees and fits with this being a vessel of war.
The fact that the Ripley deciphered the beacon from the Derelict as being a warning indicates the Space Jockey at least was benign or perhaps it was just trying to warn its own faction that it had crashed on the moon after being incapacitated by an escaped face hugger from the cargo bay below. As Ridley Scott mentioned previously the Derelict was probably carrying the Xemomorph's to infect some planet as a bio weapon in some long forgotten war and unfortunately for the Space Jockey one face hugger escaped from stasis and impregnated the Space Jockey. It must have then managed to fire out the warning beacon before the chest burster exploded from its chest causing the ship to eventually crash into LV 426 at some point.
The above is an educated guess and what I take away from the visual hints offered in Alien, which disappointing no longer seems to completely fit with where Prometheus is taking us with the humanoid engineers who conveniently happened to have engineered humans rather than being something completely Alien and ancient. I think most fans of Alien would have agreed it would have been better to have left this a mystery. Prometheus just doesn't seem dark or gritty enough to fit in with the reality that Alien depicted, it tried to be too profound and took it into the young adult action/adventure genre rather than being a serious science fiction horror like Alien.