>>3304364Yeah, that's how he intended her to be seen.
She's the best girl regardless because - unlike Asuka, Shinji or Kaworu - she grows and changes throughout the series, and always for the better. Despite being treated like science experiment all of her life/lives, she wants to be the best she can be and do good for mankind, and she actually acts toward these goals. She's traumatized and emotionally broken, having faced far worse challenges than any other character in the series, but never succumbs to weakness because of them.
Why shouldn't we care for her? Why shouldn't we want to help her and heal her?