Well, yes, but that's because all these villains have been working on the same plan, Tsuki no me, and Akatsuki was the main factor in carrying this plan out.
Besides, you are overexaggerating thinsg. "Pain" (Deva path/Yahiko) might have been a puppet of Nagato, but it was still the same character.
At the time when Nagato was revealed, we already knew Tobi ("Madara") was the villain. We never thought of the character named "Nagato" as the main villain.
Althought Tobi was Obito, he posed as "Madara" for most of the time, including telling Madara's backstory etc. So Madara was already sort of in it as a villain. And by the time Obito's identity was revealed, Madara was already back and it was shown he knew of the plan.
And Black Zetsu was never the main villain. Kaguya is. Last chapter only clarified his role as her will, but we knew he set everything up for her since he betrayed Madara anyway.
So, in short, it wasn't exactly one villain after the other.