Prometheus was very intriguing, and had a lot of really cool ideas (a few bad ones as well, but still a lot of good ones), but unfortunately it had some problems that prevented it from being truly great. I really like watching the movie, and think about it a lot, but some of its flaws are unfortunately painfully obvious. Still, I think it laid a great foundation for the sequel, and I would love to see its mythology expanded upon.
Moon is probably my favorite recent science fiction film.