The majority of the problems have not just been from the Kages, Madara, BZ and Obito were controlling things in more than one village not to mention the fact that Oro was doing his own thing in Sound village. Also Ashura and Indra have a role in how things played out so some circumstances were beyond the Kages control. That does not excuse all of their actions but Sasuke does not get to excuse some people for manipulation and not others. Pain would not have been created if it weren't for Danzo and Hanzo so there was plenty of manipulation to go around. Let's not forget that the Akatsuki as created by Yahiko had a different purpose in the beginning.
I am not excusing the Kages or making excuses for them. Some of them did some really horrendous things, but there were many more things that came into play than anyone realized.
There was plenty of manipulation going on by many people. Yes Sasuke does view them as a threat, why else kill them while they are sleeping. He does not want to have to bother fighting them. While Tsunade has done her best to make sure he is not viewed as a criminal and tried to have him viewed a a Leaf problem only, the other Kages do view him that way and would not go along with anything he would want to do. Once he helped Obito, even though it was only temporary, Ay and the others will not listen to him.
Sasuke is very arrogant so I don't think he views Naruto as a threat, but Naruto's popularity is a problem for him and since he is a jinchuriki he is determined to kill him. I would think he means to weaken him and then seal the other half of Kurama so Naruto will die. Sasuke must know that killing Naruto with Kurama in him would result in Kurama being reborn and eventually coming to get even with him.
I don't agree with what he's doing but he's trying to minimize the threats before he puts his plan into action.