Isn`t the final scene Shinji`s personal Heaven as a result of Human Complement Project?
No. Shinji was shown what Human Complement Project would be like if it was accomplished, and when he saw how fake the happiness really was he chose to stop it. He finds that Complementation is just another version of running away. He realized he would still be alone, because even he wouldn’t be there. Rei and Kaworu warn him that if he chooses to return to reality that AT Fields will once again hurt him and others again, “Fear of other people will once again return.” But Shinji say to them “That’s fine.” Further, this is confirmed in the Cardass Masters card game that states, “Shinji renounced the world where all hearts had melted into one and accepted each other unconditionally.” This is fact.
