It was not Kakashi's job to look into the Uchiha massacre. Hiruzen and Danzo knew what went down so there was no reason for Kakashi to investigate it. Hiruzen knew what Danzo wanted him to know-he obviously did not tell him that he threatened Itachi with Sasuke's life. He was part of Hiruzen's ANBU squad, if Hiruzen wanted him to investigate it he would have told him to. Itachi went to Hiruzen after it was over and asked him about keeping Sasuke safe so as far as Hiruzen was concerned it was over.
Kakashi held nothing against the Uchiha. He liked and respected Itachi's abilities and said he would make a good Captain. Obito was his friend and he spent more time training Sasuke than he did with Naruto or Sakura. Maybe he could have done more to change things but he was broken, he was just enduring and not much else.
As for Sasuke he is right about one thing, Itachi would have made a good Hokage with the lessons he had learned and tried to pass on to Naruto. Sasuke is not totally wrong, the system does have to be changed, but he's basing these decisions off of the 1 or 2 days he spent fighting in the war with everyone. The Alliance might have started because of common cause but that is no longer the only reason for it. These people, who thought they had nothing in common and disliked each other just because they were from different villages, have come together, learned to trust each other and view each other as comrades now.
Is Sasuke even taking the time to see what happens with that before he just tanks everything? The hokages have come together too and are no longer fighting amongst themselves. The have admitted they made mistakes. Should they be killed? I don't think so. At the very least Ay and Onoki should be asked to step down but Mei, Gaara and Tsunade did not cause the current situation. Mei and Gaara are trying to set their villages on a better path and Tsunade has been butting heads with Danzo and the elders since she took over. She finally told the elders she would do as she pleases.
Sasuke is right, there does need to be changes, but he took the wrong lessons from Itachi's life. This is not the lesson Itachi wanted him to learn. Itachi wanted him to go back to the village and strengthen his ties not annihilate them. I just don't think that someone who spent his time in caves and hideouts with Oro since he left the village is really qualified to say what needs to change because he's been away from it for so long.