They did a neat job of carving a path in a different direction while maintaining the horror vibe from Alien mixed with an awesome new sense of discovery that hasn't really been matched by the previous movies. The characters were interesting (especially Shaw / David / Vickers), the insight into The Space Jockey kicked ass, and the various threads they wove in there to tie it to the previous films were great.
Guy Pearce pulled a Ed Norton (from Kingdom of Heaven) there, too. If I didn't see his name in the credits, I never would have known that that was him. Awesome stuff.