>>3622949If the comment about him not understanding Rei is sincere, it's possibly because he decided early on that Asuka was the "better girl" (and I definitely remember him saying something to this effect), so he consciously or unconsciously put Rei's arc on the backburner to make way for Asuka. That would explain why Rei's character development kind of get's cut short at the end and why Anno changed her so much in the Rebuilds.
I agree she has way too many dimensions to simply be a waifu deconstruction, but I always saw it that Anno was trying to draw in symbolism about how she's something created and a hollow ideal yada yada but ended up botching it because she's still a fully developed, dynamic character.
Either way I've always had a weird sympathy for her because it's easy to see how she can ( and want to) become a "normal" human being but Anno just doesn't want her to have a natural character development.