I wanted to talk about this whole affair of Naruto being affected by Genjutsu at this point of the manga. And Genjutsu is longer a problem for Naruto, I hope Sasuke doesn't use it against Naruto as it could be have fatal consequences like against killer bee. But fortunately for Sasuke, Naruto won't kill Sasuke as he already made that clear. The same way Sasuke spared Naruto's life at the Valley of the end Naruto will spare Sasuke's life, only time will tell but I a have very strong feeling about this. Anyway back to the topic at hand.
When Naruto learns to control the fox's chakra genjutsu goes out the window. We saw it when Sasuke vs killer bee. And we saw it during the encounter with Naruto and Nagato. Nagato with his chakra tried to control Naruto's body like he does with his pain bodies and failed.
Now about the Sharingan and the Fox, a lot a people are suggesting as soon Naruto uses the fox's chakra Sasuke will be able to suppress it just like how he did in their first encounter in Orochimaru's lair. This is wrong and thanks to the new info we have on the fox it became quite apparent to me how the Mangekyō Sharingan controls the fox.
Sasuke suppressed the Fox's will which indirectly suppressed the fox's chakra and Naruto helped during that encounter. This is pretty complicated to explain in one sentence so I have break it up.
The Mangekyō Sharingan, can only completely manipulate the Fox's will and indirectly gains access to the fox's chakra as the two(Will and Chakra) are strongly connected. The regular sharingan Sasuke had at the time could not do this. This how Madara used the Fox to his dirty work from the shadows in the past. Naruto was also suppressing the fox's will at the same time because of the previous messy encounter with Orochmaru. So Naruto in a sense amplified Sasuke's innate sharingan ability to suppresses the Fox's will, in the end it was a 2v1 encounter against the fox. And as we found out recently when using the fox's chakra the fox's will wants to come along for the ride, so when the WILL was suppressed so was the CHAKRA. Things could have gotten very bad for Sasuke if Naruto wasn't rejecting the Fox at that time, as it would have been a 2v1 but against Sasuke this time. And Sasuke didn't have the Mangekyō Sharingan to negate Naruto's fox mode. Yamato would had to step in again.
What Naruto is trying to do now changes everything. Naruto is trying to JUST access the chakra AND reject the WILL of the fox. So the next time Sasuke tries something these is no will for the Mangekyō Sharingan to control or suppress. A good analogy of what Naruto is trying to do, is split the atom. (very hard lol)
Note: Notice how this works the other way too. The First hokage/Yamato(with necklace) can suppress the fox's chakra which indirectly suppresses the fox's will as they are strongly connected, this how Yamato could stop Naruto when he started using the Fox's chakra during his wind rasengan training.
It could also be speculated when isolating the chakra this could be a double edge situation. For example the 8 tails acted on this own by was using his chakra, to disrupt killer bee's chakra. Removing the will of that chakra will could now mean killer bee can't break out of genjutsu. But if this is in fact the situation how would you describe how the curse seal works? Jugo can call upon this dark chakra at will and it doesn't have a will like the fox. Maybe once Naruto isolates the fox's chakra he too would be able to use the fox's chakra in a similar manner.
You could then argue that the curse seal's chakra has a will of its own because of that killer maniac urges you experience. But this may occur because of a lot of exposure to the chakra. Similar to how Naruto with a lot exposure to fox's chakra can shorten Naruto's life span. We are yet see if there's any more to the curse than that. That dark chakra does erode your body, its quite reasonable to say it erodes the users brain too and turns him/her into a madman. Simular to how brain diseases erode your brain and you begin to lose all your memory. Jugo has these killer maniac urges even without using the chakra, so its quite reasonable to argue it's a cause and affect as oppose to the chakra itself has intentions/will like the bujj. And unlike the fox's chakra it doesn't act alone like what we saw during the fight with Sasuke at the vote.