I'm really late to the party on this one, but it's not my fault. I only discovered this page like a few weeks ago through Zarban's page (which I in turn found through Rifftrax iRiff hunting). Anyway, I'll throw my two cents in for the hell of it:
1) The Arcturians line bothered me too for the same reason. I eventually decided that it was just probably a human colony. Humans can get pretty weird over a few generations if they are geographically isolated even on Earth, so I can only imagine what an isolated colony in space would be like.
2) I thought that almost every special edition scene was something that the movie was better without except for two:
2a) The scene with Ripley's daughter was short, poingant and added some emotional resonance to her character as well as helped explain why she was so crazy about saving Newt. Also, an interesting bit of triva: The upcomming Alien game that actually looks like it -won't- suck is a pure horror game in which you are trapped in a space station with an single Alien. It's not a shooter like the previous games, and you -cannot- fight the Alien because it will pretty much murder you outright. The protagonist of the new game is Amanda Ripley and takes place 15 years after Alien and focuses on her searching for her mother.
2b) The autoguns scene. For some bizarre reason, these scene was included in a cut that exists in the various broadcast TV cuts even though I'm pretty sure it wasn't in the theatrical version I saw. Yes, I agree with all the points you guys made about these scenes but I liked them because it was an earlier indication that the Aliens weren't just animals and could learn.
Everything else, though, I could have done without. The colony scenes undercut the tension of when the Marines landed on the colony because in the theatrical cut you were only seeing it for the first time so you never had a baseline for what is normal. In the SE, the second they leave the dropship it's immediately obvious that this is not normal because you know what it's supposed to be like. Hudson's painful "badass" speech was just awkward. Even the little extra lingering glances between Ripley and Hicks towards the end that imply a little brewing romance were good cuts.
One other thing: I had a slightly different interpretation of Ripley's behavior in the hive. Yes, emptying all her guns was a tactically unsound but made sense for the character, but what prompted her Alien baby murder spree was the hatching of the egg. The look she gives the Queen after she sees the egg hatch I read as Ripley interpreting that act as the Queen trying to pull a fast one (i.e. the big xenos back off but then Queenie tries to slip a facehugger into the mix without Ripley noticing). Ripley gives her a "oh you sneaky bitch" look just before she starts torching the nest. Sadly, she then kinda goes off the rails at that point and we all know what happens after that.
Thanks for your time and keep up the good work!