By its nature this is going to spoil, and not just RahXephon, but Lain et al.

Art and Animation

Animation issues were obvious from the start. They've really overdone it on the clean look and reduced number of fill patterns, and it detracts a lot. The [background] art was beautiful and the designs clever and elaborate. The Alpha squadron's fighters were especially nice on the mecha side. Characters mostly rode their eyes throughout though. I could not tell who Kim's date was at first! So, Michiaki Satoh gets two thumbs up, Akihiro Yamada gets one. Ironically, according to the interview in the extras, Mr. Satoh wanted to do the character designs, but Mr. Yamada got the job first, so he had to settle for the equipment.

BTW, why is that that animators are generally unable to handle reflections? Has none of them gone to an art school?

This problem is so common in anime that it's rapidly becoming a pet peeve of mine.

World Resets

For some reason the following kind of story is getting popular: the hero attains GOD POWERS while the world is being RUINED; eventually the world is ruined completely and this pisses off the hero so much that he/she RESETS the whole thing.

Well, excuse me, but this is a crappy idea. Firstly, it's not how the real world works. You screwed up, you get to live with the consequences. Secondly, it's not how imaginary worlds work. There's zero escapism value in this setup.

The implementation of a world reset invites all sorts of nasty issues too. First is the scale. In Lain (and Matrix' fanon) the world is limited, so no problem. But in Dual it's not, so what happens to Mars? Second is the completeness: does anyone carry over the information? The God himself/herself does, but cannot apply it directly to minds (e.g. Lain only visits the world after the reset, but does not live in it). So, all cases seem unsatisfactory: Dual is just a joke; in case of Lain, I do not understand why restart the world at all without Lain if it was designed just for Lain to manifest; and in RahXephon it's unclear who knows what and even what happened to Mu. Basically, creators did not know how to solve the unsolvable and left it for the viewers to ponder. Good job, lazybutts.

I have fallen into their trap a bit and mused why Haruka cannot recognize herself in the painting. The Occam's razor solution is, she simply cannot remember how she met Ayato, and she cannot recognize herself cold from the back. There's nothing more to it. I cannot rememeber how I met my wife, too. But such straightforward answer robs the scene of any power it might have.

Chobits-style harem where women fall away like autumn leaves

I've read on a blog somewhere that "Ayato has to lose all that's dear to him" or something to that effect. Fair enough, that's a good story.

Shingu's normality vs. RahXephon's psychosis

I remember how I was shocked by stable characters in Shingu. RahXephon is very conventional in how everyone of consequence is defective. On that background, Shouichi Yagumo seemed starkly abnormal, a transplant from Shingu. Honestly, I thought he was going to be a gag character like Jun-kun of Nadesico.

Hihgly inappropriate Egypian attributics

These transplants from Yu-Gi-Oh betray a lack of imagination.

What was stolen from Eva

I intended to keep track at first, but it became impossible pretty quickly. It was a roller coaster all the way. Just as I would feel like RahXephon becomes defendable at plagiarism charges, something pops like the penguin in ep.11 or Vermillion shedding its armor EVA-like and ruins the whole experience.

Death and mayhem

Since everyone was a psycho (except maybe Kim and Shouichi), I really did not care for their demise all that much. They were all manufactured to show us something gruesome or deprived. The only person who I pitied was the chubby blonde chick, Cindy, a comrade of Elfy in the Alpha squad. She really didn't deserve it. Countless others were killed too, either by dolems or Ayato, but she had a face.

Miscellanea and linkage

Questions the answers to which I do not care to know all that much:

• Why god-Ayato and god-Quon have to fight at all? Maybe it's some kind of Ing-Yan dualism.
• What has happened to Mu after the reset?

Hige liked the filler episode. I think it was pretty clear how the cloning process worked even without that episode.

Avatar notes that creators did not mean for viewers to retcon the plot. I sort of figured that... (see "lazybutts" above).