Thousand Shinji: Rei was in love with Shinji even though she was his mother's clone.
However Rei does not want to tell him she is his mother's clone because she is afraid that it will kill any possibility of having a love relationship with him. On Fan ***tion-dot-net, there are around 3000 stories and more than half are about an incestous/romantic potential relationship between the two of them.
The fact that the youngest sisters are still children, maybe toddler age, when their elder sisters marry the shared husband. Still when Rei revealed her genetic make-up to him and Shinji figured out her feelings he did not seem concerned about her origins.
As you can imagine, given the Christian origins of the stories, this is a large division for the fanbase. Paying a small amount every now and then or spending a large amount in one go is different. Worse things happen in real life, of course, but still.- And then there is the fact that those little girls are expected to have happy *** video (
mydream***.com) with the man who maybe even changed their diapers.