Naruto was still put into a lower tier genjutsu by Itachi even with Kurama inside (not just the chakra), tell me how bits of chakra can stop Sasuke's genjutsu?
At the time when Itachi had placed the crow inside Naruto, he neither had mastered sage-mode nor he had befriended Kurama meaning he did not really have access to Kurama's power at will.
There is a tremendous difference in his power-level and skill of then and now. The little bit of bijuu chakra within let him blend BLL/KKG grade nature-manipulation with his most chakra consuming double-edged blade that is the rasenshuriken.
In addition, Naruto is sharing his psych-plane with all 9 bijuu. As the very key essence of breaking out of a genjutsu is to have someone put their chakra into you, in Naruto's case there are 9 different beings that can do it in tandem. Trying to put him under genjutsu is like trying to put 10 people that continuously flow each other's chakra through each other.
If Sasuke has all the Rinnegan ability he can simply absorb all jutsu so most of Naruto's jutsu is ineffective
If that were the case, wouldn't Madara be able to absorb his rasenshuriken instead of getting sliced in half?
Gudoudama is also ineffective towards Sasuke since he also has the sages chakra
We are not sure whether if Sasuke has Rikudou's chakra. All we really know is that the Sage has given them equal power. Considering how Hagoromo's eyes/doujutsu and body/chakra were passed onto Indra and Ashura respectively (Entrusting his legacy and gaining power through genetics is different), Sasuke was given the doujutsu and Naruto was given the chakra, boosting their respectively stronger prowesses.
On this basis, having given equal power, Naruto would very well then would end-up with the Rinnegan.
