Lain is actually God
There was some dialogue in Layer 12 that leads me to believe that Lain may in fact be the 'Creation God' reborn.
Lain: You could make the wired free from the devices. Lain: Telephones, TV, network... You could nothing without them. Eiri: Yes, they were born with human's evolution.
The NAVI and the devices like it that allowed humans to network, were a crude means of accessing an existing system.
This system is known as the global consciousness. It is the Wired in it's true form. The reference to John C. Lilly established this in the previous layer and it's reinforced many times throughout the anime.
Lain: A program to synchronize to the peculiar resonance of the earth in Lain: the Protocol 7. Lain: And it makes "the group of unconscious" into consciousness. Lain: Did you really invent it by yourself?
Here Lain places doubt upon Eiri's authorship of the physics that allow IP7 to work.
This creates a new assumption revealed in Eiri's next statements:
Eiri: What are you saying? It can't! It can't! Eiri: Do you say that there is true God!?
Here we see that Eiri implies that he is not a "true god" and that his power and presence is limited.
Lain: Humans have been all connected in their unconsciousness. Lain: I'm just reconnecting them. Alice: Did you do it, Lain? Lain: I did nothing. Lain: It doesn't matter which is real, this side or the other. Lain: I was in both.
We come back to Lain's statements to Alice. She reveals knowledge of the global consciousness and the lack of distinction between it and the Wired.
The power to "reconnect" people implies knowledge of them once being connected, perhaps Lain being the original connector. This is also a power Eiri does not seem to have.
Eiri: No! I'm almighty! I made your flesh in this real world! Eiri: You were omnipresent, scattered through the Wired! I gave you an ego! Lain: If I were so, what are you?
Here we see that Lain is something much more than human, a homunculus of sorts. Omnipresence also heavily implies godhood.
What he's referring to as "ego" may be 'Ego Lain' or more likely the dictionary definition of ego; as an individual person formed from the omnipresent Lain.
- Ego: "the “I” or self of any person; a person as thinking, feeling, and willing, and distinguishing itself from the selves of others and from objects of its thought."
Lain: Yes, you were a god in the wired. But, before the wired appeared... Lain: You were only a proxy god of someone who was waiting for the appearance of the wired.
Here Lain acknowledges that Eiri's power is only enabled by the Wired. The second statement is most important, because it allows the theory that "God" merely waited for the Wired to be created. Having existed prior to the Wired. The real God.
Since we've established Lain's presence as a homunculus, an isomorphic organism omnipresent in the Wired, it is entirely possible that she is God.