What specifically did you not understand? The Space Jockey's entire reason for being on that moon is directly related to the story of Alien and what the alien's are.
It left on one of man kinds biggest question, "why are we here?"It pretty much just leaves on the worst cliffhanger ever.
It's goal IMO was to answer all the unanswered questions from Alien. Where the Xeno's came from, what the being in the chair was and oh....lets not forget about explaining how humanity came to be. Lots was answered with this film, and everything that was left unanswered was done so specifically to provide a sequel. Now lets just hope that Scott really does take the rein's and it isn't butchered like Alien 3 and Resurrection were.I'm curious to know why you liked it so much.
It also makes you think, not many films do that. You really have to pay close attention and have to question things throughout to know exactly what's going on. Alien didn't really do that, it was a total scare-fest. That's where I think Prometheus really shines.
MERGED
It does explain their origins.
As for the Predator storyline, the writers of Alien had no intention of having the two cross. You can thank Fox and their desire to squeeze as much cash as possible from a successful series for that one.
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