The explanation I've always heard was that it was his response to otakus jerking off to anime characters. I.e. women who can't hurt you with rejection. This is who he sees them as.

From an article in which he is interviewed:

Anno understands the Japanese national attraction to characters like Rei as the product of a stunted imaginative landscape born of Japan’s defeat in the Second World War. “Japan lost the war to the Americans,” he explains, seeming interested in his own words for the first time during our interview. “Since that time, the education we received is not one that creates adults. Even for us, people in their 40s, and for the generation older than me, in their 50s and 60s, there’s no reasonable model of what an adult should be like.” The theory that Japan’s defeat stripped the country of its independence and led to the creation of a nation of permanent children, weaklings forced to live under the protection of the American Big Daddy, is widely shared by artists and intellectuals in Japan. It is also a staple of popular cartoons, many of which feature a well-meaning government that turns out to be a facade concealing sinister and more powerful forces.

Anno pauses for a moment, and gives a dark-browed stare out the window. “I don’t see any adults here in Japan,” he says, with a shrug. “The fact that you see salarymen reading manga and pornography on the trains and being unafraid, unashamed or anything, is something you wouldn’t have seen 30 years ago, with people who grew up under a different system of government. They would have been far too embarrassed to open a book of cartoons or dirty pictures on a train. But that’s what we have now in Japan. We are a country of children.”