REI (OFF):“Doctor Akagi is prepared to rewrite Unit-01’s personality data.”
He blinks once and speaks.
NemZ: I get the feeling this is actually Rei essentially telling him off, dismissing his whining and preparing to step up to the 01 piloting role she was meant for.
Captain Button: This scene gives me a feeling that part of Shinji's reaction may be territorial jealousy because Unit 01 is HIS Eva. Rei can't play with his stuff!
I also wonder if Rei is deliberately trying to prod him in that area as a trick to get him to stop moping around. But I can't really see Rei playing that kind of head game. But I can see Dr. Akagi trying to do so indirectly.
Kendrix: I doubt he sees EVA 01 as "his toy" like Asuka does, he finds it very frightening and calls it a beast once - It's more that he feels useless and lost when stuff works out perfectly fine without him. His Dilemma is that while he is very afraid of the battles awaiting him, on some level, he wants them to need him (so he can keep his place in Tokyo 3).