This anime teaches us a lesson that without friends, it is tough to survive. This anime is all about fighting the enemies(angels) and the personal problems of many characters. In the last two episodes it is difficult to understand that what happens to the humanity at the end, in last , they show that Shinji Ikari has changed his mind of living a world with friends and everybody congratulate him.
In the manga ending , it is show that Rei takes the form of Adam and creates a black moon, and is seen talking to shinji, and shinji ask her to stop this and make it normal. Later on Shinji is seen as an extrovert who is seen happy.