Some people have stated that RahXephon was "too heavily inspired" by Neon Genesis Evangelion. Episode 3 may be a very good source of that argument.
* You have the giant anti-mech that is fierce and sentient.
* You have the city that is supposed to be crowded, but is thematically lonely, empty, confusing the character as to what his next goal in life is supposed to be.
* You have the mysteries of what is going on in this film, perhaps something more mysterious going on at hand.
Main characters trying to live past the apocalypse.
The male protagonist has an issue with his mother, albeit it is not clone incest, even though it may have been implied through the female Alien figures piloting the monsters. You see an older woman scantily clad, possibly in a relationship with the male protagonist, a trinity.
However, RahXephon is more magical than supposedly technological/evangelically influenced in this episode, albeit the Kaiju monsters still have an interesting monster design to them.
Also, what many probably had issue with was that Evangelion's dub is much more better, whereas RahXephon's dub was pretty flat and unconvincing and philosophical of the characters in the situations. It did not immerse me into the characters as much.
It's also less otaku friendly.
MAJOR SPOILER for those who want to figure it out themselves:
TERRA is NERV, albeit I am not exactly sure what they are doing in this continuity. Perhaps, he's time jumping or something? I didn't quite get it from this episode at least. Maybe later on. NO SPOILERS please.
The conspiracies are stated more straight up rather than implied in Neon Genesis Evangelion.
I won't say any more now. Just try and enjoy these shows the best you can while trying to read into other people's interpretations. I hope you can find the sub unlike me.