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During their fight with Kaguya, Obito, or even Sasuke didn't use their Susanoo which could have protected them from Kaguyas "Bone Ash" jutsu.
Same is the case when Sasuke fought Madara (Tobirama was lying on the ground paralysed and Sasuke jumped from above to attack Madara). Sasuke could have used his Susanoo, but he didn't.
Was this just a loophole on the writer's part? Or is there a reason behind it?
Well against Kaguya yes Sasuke did use his Susanoo, obviously not for a long time since it won't be helpful, it was after that try that Obito joined them and of course, neither Obito nor Sasuke are stupid enough to waste more chakra like that. And against Madara it's pretty much the same thing, he used Susanoo against Obito but could do much (remember Susanoo is nothing but a big concentration of chakra, not fast, and not useful against this kind of opponents) so why would he try that again against Madara who, at that time, had the strongest Susanoo ever, was fast, strong, enhanced?? that's not a good strategy. That's what I think anyway.
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Earlier, Obito simply could not use the susano'o, as it requires Awakening Mangekyo Sharingan in both the eyes, but he had only one as the other one he had given to kakashi. Also the murderous bone ash did penetrate the susano'o, so it was pointless anyway. In the other scenario, susano'o like any other armour comes at a cost in form of bulk and thus sluggishness. A sneak attack that he hoped to work wouldn't.
While battling Kaguya, the Susanoo was not a good option because of her abilities. In Episode 459 of Naruto Shippuden, Sasuke was actually using his Susanoo during the beginning of the fight. However, Sasuke stopped after he realized that Kaguya's Rinne-Sharingan ability could absorb all forms of Jutsu, including his Susanoo.
Just like Green mentioned, the Susanoo is a massive humanoid projection of its user's Chakra and so the entire Humanoid avatar can be absorbed by someone who posseses the Rinne-Sharingan, and thats actually what happened when Sasuke tried to attack Kaguya with his Susanoo, she simply absorbed the attack along with his entire Susanoo.
In the case of when Sasuke came after Madara (Episode 393), He was trying to catch Madara off guard while Tobirama kept him preoccupied, and so a Susanoo would have been a bad choice in that scanrio because of how big it is and since its a massive avatar of chakra, anyone could easily sense it.
