Pain/Pein was the highest point in the series villain wise.
Not only was he set up well, but he presented himself in a very good way. He was a complete bad ass, was very dangerous, and had a back story that both explained his motivations perfectly and linked him directly to the Naruto cast.
It was prior to Naruto himself getting crazy overpowered, and still showed a great deal of skill and effort to deal with. Having Nagato controlling all of the paths at once made him very tricky and dangerous. It showed Naruto at his best, and also allowed his weaknesses to be shown and exploited.
He was also a villain you could understand perfectly well. He wanted peace, but his life was so full of turmoil and loss that he firmly believed that what he was doing was the only way he could honor the wishes of both Yahiko and his former teacher. Naruto's TNJ actually made sense in this instance, and has never been as relevant to a villain as it was here. His attempt at redemption fit, and was a great capstone to the arc. It showed how much Naruto has grown both in skill, and in attitude.
IMO, the series went downhill after.
Oro was also a great villain, but they never set him up with a great final arc to give him a send off worthy of his character. His redemption, if it even was/is one, was handled even worse.
Obito, Madara, and Kaguya just are not well done villains. They all had potential, but far too many issues with the last war arc. Nothing got the time it needed to really build or mature into anything, especially not Kaguya. Even if she'd been hinted at a few times... she just was no much of a character.
