In the Still Darkness
Rei says with certainty that she isn’t Gendo’s favorite. If his favorite is Shinji, then he has a harsh way of show it. While it’s understandable that he doesn’t have time to appear at Shinji’s school, Shinji has no way of knowing anything about his father.
Finally, Rei is getting more time in the episodes, although her role is kept at knowing what needs to be known, and doing what needs to be done, and that’s that. And, as Asuka says, Rei will do what needs to be done with unwavering determination.
Shinji’s questioning about the Angels follows along the lines of what I wonder. Just what are they? Where did they come from? Why are they called “Angel”? I also wonder how they start out so similar to a human before birth, yet quickly grow out into a creature different in form every time. The loss of power suggests that someone is out to help the Angels. Who, and why?