Dr. Nick: The famous interaction I mentioned. Rei, unsurprisingly, shows no emotion to Asuka's outburst, but I like to think her words stayed with Rei, even into version 3.0.
UrsusArctos: Since Rei 3 says "I'm not a puppet" much like Rei 2 and demonstrates it unequivocally to Gendo, I guess your case is fairly solid.
