Largest connection with the main character: Obito
Mastermind behind the whole series: Black zetsu
Madara & kaguya were simply powerhouses without much depth or much of a connection to the theme of the story [BZ was the real "curse of hatred"]. Nagato was a good villain w/ his connection to jiraiya & acting as the "leader" of the main group of villains in the story. Obito however had more of a connection w/ naruto & overshadowed nagato's position as leader in the end so that's why I believe he was better.
Orochimaru, Lol almost forgot about him.. He was decent in pt 1, but awful in pt 2.