I'm stunned by the fact I have never seen this film before, as I love James Cameron's films and his way of directing. I don't think I watched the directors cut, but nevertheless it's a very good story and I did not expect the ending like that.
What I love about this film is the human connection, individually and as a group. The characters feel very real and you create empathy to the main characters. This is a great example for film studies, as I do one myself – and especially considering it's a film from 1989. James Cameron never fails to surprise me. Also, the entire 'alien' element IS part of the story and it's not 'too much', in fact it's beautiful to watch. Especially towards the ending, if you've seen it or will soon, you know what I'm talking about.
Science-fiction can have good storylines, with well written characters and good Visual Effects. This is one of them.