If I was an "Alien purist" I wouldn't be here defending Alien 3, genius. Think before you type.
I love the entire alien franchise, even Resurrection. I'm just tired of all the butt hurt whinebags who claim to be fans of the franchise, but really only like Aliens and think it's "teh greatest thing evar" and endlessly bash Alien 3 because their ADD won't allow them to watch a great film that doesn't have a) a dozen cheesy dialogue-spouting marine badasses with big guns, b) a hundred new generic aliens with the big "boss" alien at the end or c), a & b having an all-out war.
And no, it still wasn't a massive plot hole. I don't think there's been anything established that states those eggs couldn't possibly have been there.
The queen alien using the elevator is just as if not more ridiculous than that, and neither "issues" take away from the films.
Just for your information, an Alien Purist is anyone who slams the second film for being different or someone who claims that Cameron prostituted Scott's vision, which is pretty much what you've been doing. So perhaps you should take your own advice.
To my knowledge Alien was the first science fiction horror film. In my opinion it's a masterpiece because everything worked. You had characters to love, an evil corporation, a single villain that caused total mayhem and even a Judas type character to pull off a twist toward the end. It worked so well because it was fresh, audiences didn't really see the creature and because you had a group of civilians on a huge ship, with no training who didn't know what they were up against. You can't make that film a second time.
As Khev said, Aliens was the next step in the franchise. The type of film didn't even change that much. You don't even see an Alien for the first hour and there was still suspense. The reason it worked was because it gave you the same things as the first, but delivered them in a different ways with a bit more action. The film even ended almost the same way as the first.
Now Alien 3. The production behind this film was a mess. I believe it went through 9 directors and just as many scripts. The studio raided the set and caused complete chaos and they even tried to use an actor's likeness without his permission. I don't blame Fincher for that at all, it was his first film and I'm sure he was at the mercy of the studio.
The problem with Alien 3 as a story is that it didn't give you the same elements that first two did. Other than Ripley there are no characters to love, no Judas and you know what Alien looks like. Fincher was huge fan of the original and tried to create the same fell, but it didn't work on many levels. A single Alien just isn't a threat, unless of course you kill off the only remaining Marine, add in a couple dozen dumbbell criminals and take away every piece of technology or weapon that Ripley can use against it.
You do know what a plot hole is right? When doing a sequel your story has to lineup with the continuity of pervious film. They didn't do that and it's almost as if they thought the audience was too stupid to think for themselves.
No matter what theory you go with, one egg or two, it's a massive plot hole that can not be explained. The egg that we see is smaller and it's on the ceiling of all places. Then the egg or facehugger somehow gets into the cryo room from the hanger, breaks into Ripley's cryo bed and causes a fire. Finally, if you go with the single egg theory, it lives long enough to jump on to a dog and lay another egg. This goes against everything we are shown in the previous films and it doesn't add up.
Fox wanted people to swallow this ridiculous story setup because they had ran off all the talented people. There's a reason they chose a director with nothing under his belt.