What is true is that the konoha higher up definitely had a hand in the slaughtering of the village by using itachi.
What we do know that is true is itachi life
Kushina's life
Tobirama created edo tensei
The only thing we arent sure about is what tobi said about the start of the village and the discrimination issue. We need more info before he judge whether tobi was trolling or telling the truth
First of all, thank's for the brilliant post, and for bringing up this discussion.
I want to repeat a part of my arguments that I have made in my thread about the Uchiha massacre mystery.
In this thread, a lot of people already criticized OP for relying too much on Tobi's words. I wish to add that not only Tobi could be lying, but he could be hiding important facts.
I know this is conjecture: but some people in this thread have already wondered why the Uchiha have started the plot against the village. I do not mean that they had no motivation; but they were much weaker than the rest. Isn't it strange that they would try to make a move out of such a weak position? And, even though they might have resented the distrust and the weakened influence that was a consequence, I do not think that their position was so desparate that they would have no choice but to fight.
So, a large part of the Uchiha mystery that is still unexplained is, in my view, the question: why did the Uchiha rebel?
In my opinion, they must have been convinced that they had a chance to win. And there is one person that could have convinced them: Tobi, posing as Madara.
We have seen lot's of evidence of Tobi working like that: behind the scences, making other people do what he wants. He did it when he controlled the Mizukage.
What he could have done is revealed himself to the Uchiha and offered his help in the rebellion.
If this was the case, together with the fact that Tobi was actually responsible for the Kyuubi attack (notice that here he lies to Sasuke, saying that this was a natural disaster), this makes Tobi directly responsible for the death of the Uchiha. I think that if Sasuke realizes this, he will quickly change his target ;]
But this is not all. I chose to quote this post because OP says: "What we do know that is true is itachi life".
Now that's a bit too much. We only know the version that Tobi said, plus the fact that Itachi did not deny the most important parts of it, and Danzo did not deny this as well. But an important part which is unclear is:
1) was Itachi really sufficiently motivated to kill his own family and clan?
Or did he just agree to take the blame in exchange for protecting Sasuke?
Notice that Hiruzen did not support this action, and Danzo only wanted the Uchiha's eyes. Could Itachi really have gone along with this? If so, it would really make him Danzo's puppet. I do not think so.
2) could Itachi really do the job himself? Tobi says that he helped Itachi, but there is an important problem. When Itachi learns from Naruto that Tobi told Sasuke how Danzo ordered the massacre, he says: "Damn you, Madara... So you knew..." How is it possible for Madara/Tobi not to know about Itachi's orders, if he was helping him?
The dead bodies of the Uchiha do not have any signs of Amaterasu, and there is no destruction in this part of the village that could be attributed to Susanoo or Shinra Tensei. The Uchiha seem to have been killed by "conventional means".
3) What was the role of Shisui? How did Itachi get his MS?
I would say, before we can settle the score of the conflict between Senju and Uchiha (btw, I completely agree with OP that the Senju were no saints), we need to resolve the Uchiha mystery. Can anyone help me with that?
Another interesting bit that awaits an explanation is Zetsu.
We know that Zetsu was the result of an experiment that combined Senju and Uchiha DNA. If this is true, and if Zetsu was created before the fight between Madara and Hashirama, it seems like Zetsu was the result of an cooperation between Senju and Uchiha. Considering how this turned out, nobody could really think that the Senju were any better than the Uchiha.
Same goes for Edo Tensei. I fully agree that developing this technique by Tobirama is a black spot on the Senju.