1. Get in the fucking robot
2. Be a man and accept the girl's feelings for him
3. Fuck bitches.
The legit best most simple way to save this character is to make human girl. This would be a completely different series and the Shinzo would have many more fans and it would automatically make his behavior "justified" in the eyes of Eva fans although I didn't have a problem with 14 year old Shinjis behavior anyways.
If otakus are THAT insecure about their masculinity, then I'm glad Shinji is a guy.
He doesn't need to be improved. He's perfect.