They're both terrific films and comparing the two is splitting hairs, but I prefer Alien. A few reasons.
I think Aliens is basically the same movie, only with guns and more Aliens. Cameron even basically recreates the beats of the finale, Ripley discovers there's an alien on her ship, retreats into a closet, comes out and ultimately blows the alien out the air lock.
I disagree that the space marines are more fleshed out as characters than the space truckers. For the most part, they're a collection of cliches and one liners. The gruff sargeant. The green lieutenant. The slimy corporate weasel. The quiet, competent one. This most especially goes to Bill Paxton. They're good, entertaining cliches, but they really don't exist as characters outside the context of this particular story.
I like the production design of Alien better. Nothing wrong with the work in Aliens, but I'll take Giger any day.
There's an interesting subtext to Alien of male rape. John Hurt takes it in the mouth, from a vaginal-like egg. He later gives "birth". Harry Dean Stanton gets penetrated from behind. The alien has this tongue with teeth thing going for it. Cameron essentially removes all that subtext and simply turns the aliens into space bugs.
