Even if I didn't like the atmosphere and more slow pace of the first one, the second doesn't really do much in the way of story. It's essentially the first movie, but throw in a Queen Alien and a bunch of Marines. The story/premise is almost identical. The only difference is the first takes a space horror approach, while the second is straight-up action. I can't help but see the two as being virtually the same movie but executed differently.
That said, I preferred the second when I was a kid, but in recent years the first has edged it out. Alien is a "flawless" movie. Aliens (the extended cut) is almost there.