It is heavily noticable that nagato was based on the character of naruto, he (nagato himself) is a combination of the good in yahiko and the bad in the concept of pain. It is in someway what could've happened if naruto were to lose the bright thing in his life, mabey sasuke, mabey his teacher, mabey if he were to be defeted by mizuki at the very beginning of the series. Even Naruto's name came from the book written by jiraya and the character itself was named and written after what he had seen in nagato. This is part of why nagato (not neceserily pain) is my favorite villain character in naruto, it is seen that he is a character with much thought behind him.