>>3690398Because that ReiQ spent (14?) years staring at a wall, being told to only follow orders and nothing else. She didn't talk to anyone or truly interact with anyone else all that time (didn't have any bonds) and didn't have any idea of what else to do other than stand in place and sleep in the LCL tube because, again, she only did what she was told to do.
Remember 3.0 is part 1 and 3.0+1.0 is part 2.
Only after 3.0, after Asuka tells her to do whatever she wants to do and when ReiQ experiences the world, is that she says she likes Shinji too.
It's a short kinda different version of NGE Rei II. All she knew was Gendo and she thought that was happiness, but then when she met Shinji and others, she realized she was just being used and abused.
The difference with ReiQ and NGE Rei III is that NGE Rei III can see how Gendo doesn't care about her in real time after she remembers (Both NGE Gendo and NGE Shinji think Rei III is not "their Rei" so they ignore her)
Meanwhile in 3.0+1.0, Gendo still treats the Rei clones as tools, but Rebuild Shinji leanrs and says that "Ayanami is Ayanami" to ReiQ when she asks for a name, in other words, "Ayanami" can be anything she wants to be, Rei II and ReiQ are both "Ayanami" and they are both different and that's fine