The lack of character development, as some people have posted, didn't bother me. After all, how much character development can be done in a two hour movie (that to me seemed to go by a lot faster than that)? The masterpiece
2001: A Space Odyssey had even less character development than
Prometheus. Both stories were about the actual events rather than the people, who were background material.
The
Prometheus story is told from the humans' point of view - primarily Shaw's. It is not an omniscient viewpoint, hence the unanswered questions, and I think it makes one more thirsty for a sequel or a series. The audience is exploring right along with the
Prometheus crew. I agree with PanzerMeyer that the so-called plot holes are open-ended questions and invitations for the viewers to interpret for themselves.
Shaw intends to find the Space Jockeys' home world because she can't believe they went through the trouble of seeding intelligent life just to destroy it later. Perhaps there are two or more classes of SJ's - the benevolent scientists in robes and the warrior class in the black armored suits, with vastly different agendas. The scientists want to foster intelligent life on other worlds but the warriors see this as a security threat and intend to clean up the results of the cultivation. There was probably conflict and fighting among the factions.
The race is on for Shaw and David (now the Head Android

) to contact the SJ scientists and to display an example their successful seeding attempts, something more likely to happen by going to the SJ home world.