Hideaki Anno, in an interview excerpt from the 1997 book Shizo/Parano:

"The truth is, I have no emotional attachment to Rei at all.

In the midst of making Evangelion, I suddenly realized that I had forgotten her entirely. Her very existence. For example, in Episode 7, I just happened to remember she was part of the cast and decided to add one shot where she appeared. I had no attachment to her at all. I thought that was okay. In Episode 8, she didn’t even appear. Not even in a single shot.

In the end of Episode 6, Rei tells Shinji “I don’t know what to do,” and Shinji says, “I think you should smile,” and Rei smiles. I cursed to myself when I reconsidered that scene. In short, if Rei and Shinji succeeded in “communication” there, she’s over with. At that moment, Rei, for me, was finished.

When she smiled, she was already finished, this character."