Rin's power, Rin's death, will Oro betray, how, who is the one who knows everything, how Nagato was used, what Tobi was planning to do with Sasuke, what was given by the beasts to Naruto, what will happen to Yamato, to Kabuto, How spiral died, etc. etc.
The question "where is Naruto" remains. I wouldn't think he is invisible or underground. He could be :
- in Tobi's dimension. Sent by Tobi who thought he was a clone. I first thought this option doesn't make sense as Naruto can't send himself back to usual dimension. But actually he can. he just has to summon a frog, go in his mouth, and release the summon. He ends up in frog's land.
- In frog's land, accumulating nature energy together with Karuma and sending repeatidly only clones to battle. Seems to me a safe way to confront Madara.