Is it in the eye's??

[Vagabond]

Well if Itachi is the "leader" (if there is such a thing) of the akatsuki then i can see Naruto fighting and defeating him in the future.
If not, i agree it would be pretty stupid if Naruto kills him.

[Ganesh]

i disagree, i believe it will go like this
Kakashi vs Kabuto
Jiraiya vs Oro
Sasuke vs Itachi
i don't think kisume will be a major character.

however, naruto has to have some influence on the whole story. hmm, maybe support or something not sure.