Board Thread:Naruto Discussions/@comment-1512913-20170121174919/@comment-734582-20170210101836

Georgio722 wrote: There's also another reason. Since Rinne Sharingan has 9 tomoe, and Sharingan has 3 tomoe, it's only normal for Rinnegan to have 6 tomoe (as shown with Sasuke). This means that the amount of tomoe also signifies which type of chakra they have (ie. 3 tomoe = Three Paths, 6 tomoe = Six Paths, 9 tomoe = Nine Paths). Makes sense to me anyway. There isn't really such a thing as three or nine paths.

The Six Paths refers to the whole reincarnation thing. If one is master of the six paths, then essentially you're enlightened. Hence the mastery over chakra, jutsu and elements. There's no such thing for three or nine paths, it's just used as a numerical theme. this includes things like six as an incomplete number (Nagato has seven paths, the magical number), three as a stable number (or trinity) and nine as a trinity of trinities.