1) So who exactly are Space Jockeys ? It's never fully explained what these things are and their true nature. We have bunch of characters making their own 'assumptions' under duress and then we have this android that seem to have its own agenda filling in the blanks. And what exactly did David say to that Engineer that it tore his head off and pummeled everyone else ? Really wish it was explained more thoroughly.

2) What exactly is the black goo ? How come it seem to kill some people but possess others ?

3) Is Vick an android too ? I mean surely there must be more to Theron's character than just a convenient suit on the deck. It be nice if she was but then again to what purpose ?

4) Unlike the original Alien, the characters aren't just miner contractors, these are 'powerful' individuals - scientists, tech mogul etc .. the pride of the human race so to speak yet they seem utterly incompetent. You don't try to pat a cobra on earth so why would you pat one in space ? Geologists getting lost in caves when they are equipped with advanced communication devices. People going off shagging when they are on verge of discovering new knowledge and power. It seem the only person who was 'working' at that time was the android.

Is Prometheus really a prequel or a canon ? It can't be the same ship that was in Alien. As you pointed out, the engineer of that ship died in its pilot seat where as the one in Prometheus died in the shuttle.

Ahh so it is a different planet and ship after all. Come to think of it, the mining ship was only diverted to planet 426 after they intercepted a distress beacon. I have another question, do you think that base on the planet 223 is a military installation as said by that ship captain ? If it is one, why would they leave a road map of it on earth ? Seems like severe tactical flaw to me.

Now i'm probably just over thinking things but that scene where David watched the hologram of the Engineers in the navigation room - there were four of them, it almost seem like it's suppose to symbolize the four horsemen of the Apocalypse. When the time is right, they will descend on earth and wipe everything out with their bio weapon of mass destruction.

Yeah i do think it's a bit far fetched in regards to the horsemen .. was just my active imagination of trying to piece everything together because as you said if the engineer did come to earth to observe and teach, then maybe they too were the source of our religious aspirations. It really was anti climax that the characters didn't get to properly communicate with the engineer.

Anyways, back to the military outpost, i really do wish it wasn't so ambiguous. I think you may have a point about the black goo that it may not naturally be a weapon - kinda like virus - on its own it may not be that harmful but if weaponized it can be deadly. So perhaps it was just some research/storage facility that keeps those black goo. That still doesn't explain why they felt it was a good idea to leave behind a road map that points to its direction. It's just seem so bizarre.