The other thing is, while in Sage mode, Naruto's entire body is infused with nature chakra. Genjutsu is the manipulation of a targets chakra in order to confuse or deceive the target.

What I mean to say is Naruto may be flat out immune to Genjutsu in Sage mode, or at least immune to non-nature based genjutsu. Beyond that, you know that when Naruto faces off with Sasuke he is going to be 'cross eyed'. He will have his chakra supplemented with the 9 tails chakra (since he will have learned to control it by then with the 8 tails help) and will, as a result be able to draw on a ton of nature chakra to suffuse his body.

Basically the manipulation of that chakra by an outside force may be impossible. Like moving a mountain.