Reasoning behind the line "I won't be your puppet."

[Rahaquiel-2D1S]

Since Rei = Yui (sort of), maybe Rei was mad at Gendou for being mean to her "son". Since Gendou left Shinji so he could get back to Yui, Rei/Yui realizes the trouble that Gendou has caused to try to get back to Yui.

[Legend of the Past]

Either that or she's mad at him for manipulating her for, at least, 5 years.

[Reichu]

Keep in mind the FULL context, which includes...

***
Rei:
I'm not your doll.

Gendo:
Why!?

Rei:
Because I'm not you.

***

("Doll" can also be "puppet".)

There's also the rest of the "doll" motif in NGE to take account of. Everything's part of a bigger equation.

[Ornette]

Keep in mind, this is the 3rd incarnation of Rei, since the personalities of the first 2 are different, it isn't much of a leap that the 3rd is also different. That together with the knowledge of what she really is (thanks to Kaworu), I'd say that was a random variable. Plus, Gendo was forced to put his 3I scenario into motion because of the invasion. It could be the case that his plans involved a more carefully timed and monitored process.

[ObsessiveMathsFreak]

Rei:
I'm not your doll.

Gendo:
Why!?

Rei:
Because I'm not you.

It's interesting to note the implication of the dialouge here. Rei has been Gendou's most loyal lacky, following his orders without question. A "Hai"-man in every sense of the word.

But by her statement here, she seems to say that to follow orders would not simply to be another of Gendou's puppets. Rather it would be, to be "You", i.e. "Gendou". Perhaps Rei is implying here that if she obeys now, she will become a mere appendage of, or indistinguishable from, Gendou, and lose her own self, her stated feared in episode #25. Maybe this is another subtle hint at her fate under Gendou's plan? After all, moments before we have seen the two morphed together.

Of course, from a character perspective, it is a good highlight of just how subservient to Gendou Rei has been. Methaphorically she really has been little more than an extention of Gendou's will. She has lived to serve him, and for nothing else. Perhaps she has seen her very existance thus far as being akin to that of a part of Gendou's body, and her refusal would be expressed through that.

I think there could be a few layers of meaning in that line. "Because I'm not you."

[Reichu]

I think there could be a few layers of meaning in that line. "Because I'm not you."

I remember posting something about faux umbilical cords and "Mama Gendo" once that seemed to make some kind of twisted sense.