If Naruto does end up with the Rinnegan, it will probably go something like this:
Naruto and Sasuke fight-
Itachi shows up on the battlefield-
Sasuke will become enraged that his brother was dragged into the war as a dead corpse and change sides-
Sasuke fights with the good guys and gets his but handed to him by either Tobi or Madara-
Sasuke gives Naruto his life energy or something, to give Naruto the Rinnegan powers. I doubt this will anything like Kakashi and Obito, since I don't see Naruto taking out his own eyes when all he needs is Sasuke's DNA anyway-
If Naruto doesn't get the Rinnegan, it will go something like this:
Naruto and Sasuke fight-
Naurto has to make a "Hokage's Decision", and choose to save the village by killing it's No.1 threat-
Naruto kills Sasuke-
Somewhere Itachi kills Kabuto, thus killing Madara-
Naruto fights Tobi-
Naruto kills Tobi-
I personally don't think Naruto will get the Rinnegan, as he really doesn't need it. More than likely the 9tails will end up fully cooporating with Naruto, which will give him all he needs to beat Tobi. Naruto is clearly stronger than his dad at this point, and the 4th could've beaten Tobi back then if it werent for having to deal with the 9tails. I just don't see any reason to give Naruto the huge advantage of a Rinnegan.