Thing is Madara had the people as the virus since it was people who took chakra that was suppose to connect people and they used it to fight instead. It was people who saw the Bijuus as nothing but weapons when they only wanted to be left alone and caused the Bijuus to hate Humans. Obito, Madara, and Kaguya's plan was aimed at the people not the Bijuus; Sasuke is only blaming them for what others made them do. As for the Kages, he wants to take them out for what the old Kages have done, he doesn't know anything about the bad stuff some of the Kages (A and Oonoki) did nor does he care that they want to change how they did things and try to change the system.
Also the Kages don't have the actual power, the feudal lords do. The lords all rule their respective nation (wind, fire, lightning, rock, mist). The villages are just the largest ones in their nations, there are other villages that are all under the lords rule. When a Kage gets elected the council nominates people and The Lord picks amongst them. We see the lords all talk about rather they agree about the Alliance even after the Kages agreed on it.
Agreed Mate.
I should ave thought of that.
Humans really are the virus.. If they hadn't picture the tail beast as force of weapons Maybe NV'd been a better place!