I've rewatched all of these films over the past week or so.
Alien: Looks amazing, still easily the best film in the franchise. The only one to really nail Ripley's character as well.
Aliens: Looks so much better but I'm kinda tired of JC's formula. It has its moments and is pretty good for what it is, but I still hate what he did to the aliens. In Alien, they're almost mythical creatures and carry an aura of mystery and dread. In Aliens, they get mowed down by the dozens and are fairly boring. The whole queen thing is also much less interesting than the reproductive cycle that they hinted at in the Alien Extended Cut. Ripley's character is also a bit off. Newt is incredibly annoying and only there to showcase Ripley's maternal feelings. I greatly prefer the awkward, loner Ripley from Alien but maybe that's just me.
Alien 3: The extended cut is pretty good. It looks great and has a lot going for it. It's the closest any of the sequels get to nailing Ripley's character and it's wonderfully bleak and depressing. It has some amazing visuals as well, the few shows of the planet's surface are amazing.
Alien Resurrection: Not an Alien movie. It's goofy and comical, it's fucking stupid, it's just not an Alien movie. I don't blame Whedon or Jeunet, they just did what they do. I blame the studio for hiring two guys whose style does not fit the Alien franchise in any way. This plus AvP prove that Fox had no idea what the series was or how to manage it.