Ooh! The "literal"-ness of that suddenly makes a whole lot of sense of the "Who made you God?" / "You mean there already was a God to begin with?" exchange. Eiri's power comes from the amalgamation of his personality withthe Deus Est Machina Trope itself!. Very meta.
At first it may seem a little strange that Lain, a middle school student with no apparent training or experience in computer programming can become the best computer hacker in the world in a couple of weeks, at most. That's kind of the point.
A meta-example: An article in a 1999/2000 issue of Animerica indicated (roughly) that writer Chiaki J. Konaka's goal was to create a series that wouldn't be received the same way outside of Japan that it was within it. Hindsight now tells us he failed in that regard— most everyone goes "well, what the hell was that all about?!". That's not the Fridge Logic. What is, however, is the fact that he wanted to divide people's opinions about a series revolving around the concept of everyone being, on some subconscious level, connected. Self-defeating, don't you think?
Well, perhaps he succeeded partially. While everyone may still get the concept, there will always be someone who has a different opinion, or interpretation on it. And because of the nature of the show, chances are no one is going to be completely divided up over it and is open to any interpretation as long as it makes sense to them.
Early in the series Lain appears to be the sort of befuddled person who is frequently described in the American vernacular as "isn't all there". After a while it becomes apparent that "isn't all there" is the literal truth — Large parts of her are in the wired.
At one point, Lain has smoke emit from her fingers and fill the classroom. It is in fact a fairly typical schizophrenic hallucination to perceive yourself emitting ectoplasm from your body. This, along with many other incidents in the early episodes are foreshadowing to the assumption that Lain is mentally unstable.
That moment when you realize Lain's parents expected (hoped? planned?) Lain would be shot and killed at Cyberia - they were so sure the "playing house" charade was now over, that they moved out in advance of... oh, crap, she's fine?! After that, Lain's mother always has this "why are you still alive" look on her face when dealing with Lain...
Wait, are Karl and JJ the same person? Is Mika also an AI housed in a clone? Did Taro just slip Lain an Accela during that kiss? How many different people have hacked into Lain and used her to their own ends? Did Lain just murder all the Knights, and if so, which Lain did it? Did I actually understand any of this?
In a bit of Fridge Logic, what exactly is Mika doing there? I mean, once you find out that Lain's family is fake, that begets the question of why they apparently went out of their way to include an apparently normal teenager, especially since, by most appearances, she wasn't in on it.