Yeah...
I know what you mean with David offering to help at the end. That's a bit tricky to read into because there might be different reasons or motives. If there's anything we can take into account from the original Alien-movies (first and second at least), it's that androids are certainly not trustworthy, and they don't seem to care about human casualties. When David mentions that there are more ships, maybe he was hoping for them to run into another space jockey, or a snake-like alien, or whatever that would "take care" of Elizabeth, or maybe he just wanted them to go back to earth. Seeing as he was in pretty bad shape, it's possible that he thought that he could get repaired at earth, or something.
As for the space jockey attacking them, I think my theory about the space jockeys being divided into two groups would make sense. One group of the space jockeys were proud of the humans, they left clues on earth so that the humans would find them, but the other group were more evil, or at least didn't care about a lower form of life. That would explain why the space jockey attacked them, if he was under group number two. But as I also mentioned, we didn't get to hear what David actually said to the space jockey. We heard what Weyland wanted him to say, but if my theory about David's "hatred" for humans has any truth to it, then it's quite possible that he told the space jockey something completely else, possibly taunting him.
There are indeed a few questions they could answer, but I also think that leaving a few things open is part of the charm. It creates speculation and buzz, you get to fill in the blanks yourself. While I like getting answers, people have spent over 30 years wondering about the origins of the Alien-race, who and what the Space Jockey was, and how it all started. Now we got some answers, but new questions that we can speculate about until the next movie.
In one way I thought the urns/vials made it silly because we already have the Xenomorph and it's lifecycle, and it just became a bit silly to me when it was created in the way it was (Space Octopus rapes Space Jockey), and that was that. The urns/vials still remain a bit of a mystery to me, what do they exactly do? They turned one of the scientists into a crazy alien/human-hybrid, but exactly what it was, that remains a mystery.
On the other hand, I think that the original idea for the Alien life-cycle was cooler then how it turned out to be. If you aren't familiar with it, before James Cameron introduced the whole "Alien queen lays eggs > facehugger > chestbuster > xenomorph/alien queen"-deal, there was an idea where humans that had been victims of the alien would become eggs themselves, their bodies would just sort of wither away and become new eggs. I think that was both creepier and in one way more logical, and I believe it's explored in the Directors Cut of Alien.