Shinji's father lack of attention to him and the death of her mother left Shinji to develop a restrained and quiet character.
However, Shinji is always seen trying to change himself unlike Rei who always seem to be the same.
Without anyone to care for him, Misato takes him in and acts as his mother/sister/friend who helps him a lot in finding the right way.
Shinji feels a deep hatred to his father who has neglected him since childhood and is using him as a tool for NERV.
On the other hand, he feels strangely attracted to Rei although he doesn't know why.