The revelation that Shinji didn't have any trouble thinking of Rei as a person after finding out what she is, and in fact still had a crush on her and was actually trying to ask the Doctor for advice on how to admit it to her. He no longer has a crush on her, but that's because he found out whatelseshe is.
The Doctor trying to convince Rei to consider herself her own person. She admits that the prospect of autonomy terrifies her, before the Doctor reassures her. Never has the act of taking a jelly baby meant quite so much.
Rei, of all people, becomes quite protective of Shinji after finding out that they are, genetically speaking, brother and sister note (possibly closer, as the Doctor notes that their DNA match is close enough that a "X-chromosomal clone's just about as likely...") (and that the reason Shinji has been avoiding her isn't because he thinks she's a threat, but because he's a bit embarrassed he had a crush on his sister):
Before Episode 10, The Doctor and Asuka never truly got along. Their first impressions of each other were nice but that was it. However, in this episode, it's the Doctor who motivates Asuka to move her EVA. Not just by telling her the stakes are higher than she thought, but by telling her that she is better than she thinks she is. He tells her that he's read her thesis paper, acknowledging it was completely wrong but the good kind of wrong. She dismisses it with a small smile she couldn't keep off her face.
During Episode 11, when Asuka starts going on and on about how she will have justice and Shinji will feel her wrath, Rei hits the emergency stop button, turns to Asuka, then, without displaying any emotion, tells her that if she willingly causes Shinji any physical harm, Rei will kill her. She does promise Asuka that, if it comes to that, her death will be painless. After Rei leaves, Asuka notices that she pressed the emergency stop so hard that it cracked the screen. She did so with one finger.
