Why didn't Nagato give Naruto his Rinnegan?
Well if you think about it,

Would Naruto accept the Rinnegan, i doubt it...

Who would train him to use the Rinnegan... (Jiraya's Out Of The Picture :c)

Would the Nine-Tails React So Kindly To Naruto Getting Former Madara's Rinnegan... He's already angry to losing to Naruto, with his hatred with Madara on top i think that would make him think that Naruto is going to become the next Madara... Yeah that won't end well. It also messes up the story as Naruto probably won't be able to build a friendship with the 9 tails later...

Who would revive basically everyone in the Leaf... With Naruto having no clue how to... This messes up the story.

(This is a might 50/50) Saskue wouldn't be too happy with Naruto basically getting a much, much, more advanced Sharingan and he would probably focus his time getting a Rinnegan himself... Which messes up the story...