Now since certain forum members are dying to debate this issue (so rightly so, that they'll invade every other thread with this topic), let's have a thread for it. I have actually done some research regarding both movies, and the result shows.
Not only is Alien theoretically the better and superior movie, but it actually is also more complex without shoving questions and answers in your face. I will quote sources and link examples later on, but for now just stick with me.
Prometheus is a brilliant science fiction movie, that is quite affected by it's shortcomings. It's pacing is very flawed, the characters with some notable exceptions are cliched and downright mechanical at times and the structure in which the movie asks us these questions is very much wrong. You don't propose questions to the audience by having the main character ask these questions and having them in the cover of your movie, the movie must make you (the viewer) unconsciously ask these questions to himself.
Now for all it's flaws i still love the movie and find it one of my favorites of the year, so what does Alien do right, that Prometheus don't.
FIrstly, atmosphere, the movie draws you in from the first scene and never lets go. While prometheus is jumping all over the place, Lost-flashback-style, Alien stays with you on the ship at all time. And the claustrophobia and dense atmosphere is incredibly palpable from the first scene.
Then, the tension building. Prometheus tries to do it, but fails to deliver, when the creatures themselves are just killing mechanical vessels we don't care about. No, not David, that's the mechanical vessel we do care about.
When it comes to philosophical questions, one could imagine prometheus has the high ground, but maybe Alien has more to it, than a single glance shows.
You see, Alien made you wonder who the xeno was, who created it, who the space jockey was, who Ash was working for, would androids feel fascination or maybe an attachment to these things, and it made it all without any character stating it so.
Now prometheus on the other hand is constantly spurting out lines of dialogue like: "This is what i chose to believe" and "Mortal after all". Just so we are kept in the line of thinking with the characters. Now that's not bad per say, but not an ideal story telling method like Alien had.
For more on the symbology of Alien i will now attach a video file, that i suggest that you guys watch:
There is also this article that might add some interesting ideas:
Moving on from the question's angle, how does Prometheus fare in cinematography.
Well quite brilliantly to be precise. The movie has sharp visuals and stunning audio.
It's brilliantly shot, and has groundbreaking special effects. Oscar worthy material.
But then again so did Alien.
So both movies have a 10 here as far as i'm concerned, to the next one.
The pacing. And now, that is the big big difference between both movies.
Prometheus struggles with this a lot. It starts out epic, then moves for the temple-exploration-indiana jones approach, and then tries to look and feel like Alien, not succeeding because the whole way from the ship to here, makes it not have Alien's pacing. It has loads of flashbacks and is constantly trying to yank you out of space and that bloody planet. Like it doesn't want you there.
Alien never did this. It was lost in space with no one to hear you scream from the word "go". Without so many distractions, the filmmaker could then play with your fear and with your mind, way more easily than what Prometheus did.
And that is why scenes like this make you go, WOW:
And scenes like this make you go, MEH.
(Even though the music is kind of badass)
Now, well, now go ahead and discuss.
Warning: Please read everything that i wrote and watch the videos i linked. Without those, we can't have a serious argument. I will not have this thread turn into a troll contest. If i notice any of you bad boys pulled the "didn't read" trick, that's it, no more argument for you, i will seriously not respond. Now i know, i do know, that some people are gonna disagree with this thread. And when they do, please be civil about it and have an open mind.