The idea that she was "deliberately unappealing" or was some sort of meta-commentary on Otaku. I've looked into this. There's no basis for that. Gainax even made their own Rei porn games you can buy. The opening shot of Rei in the TV show is a close-up on her tits & crotch. Gainax created "Rei smut" in the first place. The idea that they then were all high-and-mighty going "look at you losers, being attracted to the sexualized girl we created! Shame on you!" What a lot of shit. The guy making soft porn doesn't get to say that.
You can't equate corporate actions with the authorial intent of the creator. Plenty of creators have had companies do things to their characters that they didn't approve of. That's the whole reason for the creation of Mickey Mouse: Oswald the Lucky Rabbit got hijacked because Walt wasn't strict enough with his copyright paperwork, so Walt had to make a knock-off of his own creative progeny, a la Mighty Number 9.
It's true that Rei is sexualized in the show itself. But the way in which she is sexualized is accentuated by her passive nature. Perhaps she was meant to make the viewer question why he was attracted to such a character. Maybe Anno really did fetishize her because she was meant to be a representation of unhealthy otaku fetishism. Toward the end (including the End) of Evangelion, much of her characterization is turned on its head. Maybe that's to make the viewer assess whether or not he is more or less attracted to her after the transition, and question if her submissive demeanor made her more attractive to him. A lot of Anno's legendary contempt for otaku is just fan speculation, but as they say, "Anno has no bloody clue; fanwank something." Make what you want of the series and of the characters, because Anno sure as hell isn't talking.
(my avatar's resemblance to Rei is entirely coincidental.)
ANYWAY
I've started watching
Retarded Dragon Girls Zettai Bouei Leviathan. Someone told me it read like a D&D campaign, with the way characters act, and I'm definitely seeing the resemblance. Not as obvious as Slayers, primarily because it isn't a Gygaxian fantasy setting like that show, but still pretty clear. This looks like it's going to be a fun ride.