Lain is so much fun. It's probably been 8 years since I last watched it, but it's one of those things that stick with you. I love Gnostic cosmology so a scifi version of the Sophia and Demiurge story is pretty great. The contrast in atmosphere is pretty amazing too and does a great job of sort of illustrating this whole idea of the deficiency.

Neon Genesis Evangelion (VAGUE SPOILERS AHEAD!) has some similar ideas running through it, but it leans on Kabbalah a bit more, even going so far as to repeatedly display the tree of life. It focuses more on a representation of Yeshua in Shinji than the representation of Sophia that we see in Rei and Lilith. Lain, meanwhile, has no discernable Yeshua figure, opting for a comparatively autonomous Sophia or maybe just a different form of syzygy.

Fun stuff at any rate! Not a boring cosmology to base fiction on!

If this entire post is gibberish to you, I would strongly encourage you to delve into Gnostic mythology a bit and then take a second look at these shows. You'll notice the same themes in some other fiction as well!