I think Lain fell victim to what a lot of things like it did. Consider for a moment that the Internet as we know it today didn’t really exist at all, yet Lain hit the nail on the head with this down-the-rabbit-hole alt-net shit, the hyperreality where the Internet is realer than real life to people, and so on. It got an uncanny amount of things right, especially considering the date of its release.
That’s not really that revolutionary an idea today, but consider presenting that idea in 1998, even with the plotholes and other flaws of the show.