I really don't see how this is a matter of intellect though. Sure, if you're smarter, it'll be easier to figure out its specifics, but Naruto is still no idiot at that time, he did eventually become a Hokage after all, and that requires a certain level of competence and smarts, and for what he may lack he has the clones to compensate for it. You said it yourself, Kakashi himself only learned of his Mangekyou mid time skip, but had it mastered by the end of the war. Its hard, of course its hard, but its far from impossible, especially for someone as talented in the learning aspect as Naruto.
I'm not saying that Naruto is an idiot that's why I said Jiraiya himself wouldn't be able to use those eyes. Even Might Gai too.
Intellect is needed for highly advance genjutsus like Jiraiya said and the sharingan is an ocular eye that is known for the mastery of all high level genjutsu. That's why the
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If not for Tobi coming in to teach nagato (a very adept shinobi) he would've never been able to use the power of the Rinnegan in the first place. So unless Naruto has that Uchiha to teach him, his chances are as good as Nagato trying to learn the power of the rinnegan on his own. You understand what I mean right? There's a reason why Sasuke entrusted Kakashi with his rinnegan instead of Naruto if Sasuke ended up dying from blood lost. I'd give Naruto's intellect of being on par with Hashirama if anything and he has more experience with the rinnegan more than Hashirama yet he's still not fit for it.
It's not downplaying Naruto or anything but it's just showing you how really good kakashi is with just about anything.
Physical Energy is what makes up chakra, alongside Spiritual Energy. Seeing as Naruto's reserves are famously massive, that should hardly be a problem.
No I mean like it literally consumes your physical energy. Nagato who's genetics that allowed him to use the rinnegan so well still had his physical energy ripped from his body. Even if you have chakra the toll is still on your body due to side effects and what powers you use. Gedo arts demand a lot of life forces from the user along with chakra especially when you are not genetically adept to wield an ocular power.
Example would be when Nagato summoned Gedo mazou and when he used village size Shinra Tensei. It consumed his life force and shortened his life span despite having chakra left to use 5 pain abilities in konoha.
Well, she did use Preta Path through her Sharinnegan to absorb chakra, right? I mean, I assume that, but I'm not sure if it was confirmed to be that or if she did so through other means.
Alright it wasn't preta path or anything. The last person to use Gakido is Nagato because he created that power but the generic Six path power and the power of the Rinnegan is to absorb chakra and or Ninjutsu.
Considering that Kaguya in her cocoon state (gedo mazou) can absorb entities worth of chakra such as the bijus, it's reasonable to assume that her in her full form can do the same.
Like Gakido cannot absorb shadow clone jutsu but Kaguya was able to absorb Rsm Naruto's shadow clone jutsu completely gone in her unstable form.