Board Thread:Naruto Discussions/@comment-25369463-20140928140825/@comment-1512913-20140928170837

This is my take on the whole Rinnegan mess. There's just 2 versions of the Rinnegan:
 * original with tomoe, thus with "Sharingan" powers
 * devolved tomoe-less Rinnegan

The color I theorize simply indicates if the eye is focused on Ninjutsu or Genjutsu. Only red Rinnegan in my opinion can cast Infinite Tsukuyomi, while only grey Rinnegan can use Six Paths Technique.

For Sasuke's 6 tomoe, in my opinion he actually has 9 tomoe, since the other 3 are in his Sharingan, so his Rinnegan isn't missing anything but having 6.

Therefore Sasuke's Rinnegan is on par with Kaguya's in terms of "evolution", just is Ninjutsu focused like Hagoromo's.