Hmm? I wonder if Shinji would have been more liked or less liked if he had been a girl?
People would be less double standards with Shinji and Co situation, every adult in the series range from uncaring hypocrite to malignant shithead, with no survival option for the pilots. This put the hilarious twist that by running away, Shinji could keep some degree of mental health and dignity, before an Angel get to clean the board, what is looking better for mankind compared with Seele, Yui, or Misato in rebuild have planned.
To be honest, Misato was always shady in the series, Shinji was her revenge tool, with the ocasional "I'm so bad, woe is me" , manga pulled a gun on him, and Rebuild is her removing the mask of being a caring person.
It was clear that if she was going to choose between to stick it to the angels while throwing Shinji and the world under the bus. Or being a decent human being, 9 out of 10 times everyone else was going to be throw under the bus.