The "Hideako Anno hates the fans" point is actually more of a creepypasta theory than something he actually said. What he actually said which is the basis of that quote is taken out of context. The context was basically "mainstream Japan sucks, you see businessmen on the trains reading comics and porn. Back in the good old days, men were men". And who he blames for the decline is the post-war US occupation of Japan which infantilized Japanese males. So it's basically a crochety old fart pining for the good old days of fascism "before the war", and his disdain was for mainstream Japan as a whole, not any particular subculture or his own fans.
However, it is true what they say about the hair/eye color scheme. It was basically random. The character artist came up with the look of blue hair girl (oh that's right, Rei) because he liked some Jrock song called "the girl with white bandages", and he basically drew the same girl from his own manga, except with the bandages. She had brown hair. Anno liked it and used it in the show, except since Red hair girl already had red hair, he asked for a contrasting color scheme, so the guy just inverted the colors. There is no great theory behind any of the NGE shit, it's all random shit people threw together.
Trying to read some deep meaning into what Anno made, is in fact just as wanky bullshit as "which girl is better".
Also btw, Gainax is also known for pioneering a method of boob-bounce animation now known as "gainaxing" and a little after NGE they sold Rei/Asuka porn in the form of a NGE strip mahjongg video game (Gainax also made video games in house) as well as pervy artbooks of Rei/Asuka. Basically they started as pervy fan artists who created their own studio, and stayed pervy the whole time. There is no commentary on pervy Otaku, those guys were pervy otaku.