I think Alien is the superior film - it actually terrifies me when I watch it and feels real in it's treatment of space.

But the real comparison is better realized when looking at Ripley's character. Here is how my friend described it to me on Facebook last week when we were discussing Prometheus.

"The first could be specifically about Ripley's genesis as a feminist icon in Alien. Aliens turns her into a codified masculine heroine, 3 tries to remove her gender markers, Resurrection turns her into a monstrous maternal figure"