...and what about Moon? There were no un-answered questions in Moon as far as I'm concerned.
Total Recall, mainly referring to the sequence with the "recall corp guy" who is trying to get Arnold to swallow the pill because the entire movie thus far is all a dream in his mind. At the end of the movie it's still not clear if it was all just a dream or if he is actually in the real world. I believe in the book it's made clear, but the movie leaves it unanswered.
Moon, I felt this was VERY similar to Prometheus' ending. Both movies have the main character flying away to visit his/her makers to get some answers to some obvious questions. Both movies have questionable small details with possible answers that are not handed to you by the movie. For example the assumption most viewers have about Moon is that clones are used to save money, but it's never really spelled out and some people might not agree. Why not use robots, why not just use a regular employee? Similarly, in Prometheus there is the question of why did the engineer try to kill all the humans. I think the simple answer is that when he went into hibernation the plan was to go to earth and wipe out the humans, and here they are now in his ship? Clearly they are the enemy and whatever happened to interrupt his mission he had to do what he could to complete it.
On the other hand, after seeing Prometheus my girlfriend really wanted to see Alien. We finally rented it on amazon video and watched it last night. I won't say I didn't like it, I did, but it was hard to watch in parts. The movie starts very slow and the audio production standards aren't anywhere close to modern movies, it was hard to understand some of the dialogue in noisy scenes. My girlfriend literally fell asleep during the early part of the movie before the Alien hatched, because it was all so slow. After the Alien hatched and is seen the second time, it was like deja vu from Prometheus- how did it grow so big? What was it eating?
All in all, it felt like the inferior movie, when compared with Prometheus. I think a lot of the posters here who hate Prometheus are just seeing Alien with rose colored glasses and can't see it for what it was. All movies have minor flaws, and sometimes not everything is spelled out, Prometheus is no different from Alien in this respect.
You could only love this movie if you never saw alien/aliens and never saw the previews/history of prometheus calling it a genre defining masterpiece.
I feel like the reverse is true. It was very hard to watch Alien after seeing Prometheus.
edit: However, I do agree as far as previews. I avoid previews for any movie I plan to see, nothing good EVER comes from seeing previews, unless they convince you to see a movie you otherwise wouldn't even consider. Any preview calling any movie a masterpiece should be immediately disregarded. Does anyone take those statements seriously? I go into a movie expecting nothing more than some mild entertainment for 2 hours. If it ends up being better, it's a pleasant surprise.