Well, I agree that it's good that they didn't make it an Alien 0.5, but instead "its own" movie as you said, what I meant was that it started out as a prequel but they changed it so it wouldn't be, and I think it would have been even better if they hadn't changed a lot of stuff in the middle of it. Scott only has himself to blame because as soon as people started asking about the project and he said that would be a prequel to Alien, then he had opened the box. There was no way of closing it after that, and it was easy to see in every interview with him after that how he slowly wanted to turn focus away from the Alien-movies and give the movie some space to be something else, but by then people already expected Aliens and other stuff.
I agree that it opened up possibilities and questions to be answered in a possible sequel. What exactly happened at the Engineer-station before Prometheus got there? Did the engineers manage to create/encounter the Xenomorph before? (we have the painting after all), and what happened with Dr. Shaw eventually? I'm not sure how they would take the whole Black Liquid-part further, to me that was much less interesting than the Alien in the original movies.
It was great that we finally got to see more about the Space Jockeys and learn more about them. Scott said himself that it was one of the big mysteries of the first Alien, and he is right. One problem for me is that I was much more interested in the Alien-aspect of it. The Space Jockey was fascinating, but what did they use the Xenomorphs for? The origin of the Xenomorphs and so on, there was a lot of focus on this in the early draft of the movie, but it was apparently scrapped completely.
I don't really care much about the philosophical aspects of Prometheus. "How was life created on earth?" and similar questions, I don't really find that aspect of the movie to be very fascinating, I just want to see a good sci-fi movie really.
So my thoughts on Prometheus can be summed up that I really liked the movie, and thought it worked well on it's own, and I would be excited about a sequel.
Still, being the huge Alien-fan I am, it's still disappointing that some mysteries probably never will be solved. Apart from the origins of the Xenomorph, I was always very fascinated by the signal they received in the first Alien. Who left it there? Did anyone else encounter the ship/eggs before, and what happened? In the end I would say that Prometheus succeeded in being a good movie on its own, but didn't succeed at being related to the Alien-movies. As far as I'm concerned they could have left out Weyland Corp and the Xenomorph all together, but if they would have done that, then probably about half (or more) of the profits would have been gone.