I want an arc focusing on Danzo. We keep getting told about how ruthless he was, yet we are shown very little. You know you have to be a serious badass to be known as ruthless in their messed up world.
Basically, I'd want to see more about his ideals, his organization, how he thinks and why. I want more knowledge about his and Hiruzen's relationship (he clearly respected the man). I wouldn't mind being shown an alternate path, one where he continues to be Hokage, or even one where he manages to kill Sasuke. Or, just flesh out Danzo's character a bit more, and have his death have a little more impact - Sasuke assassinated the current Hokage and everyone just shrugs it off. Seriously, were there any major ramifications of Danzo's death?
Other than that, if I could just add an arc at whatever point in the story, I'd show a lot more of the Konoha 11, both in part one and in Shippuden, but especially in Shippuden, for obvious reasons. More interaction between the teams we rarely see, like a collaboration mission - Why can't they be sent of to warn the Jinchuriki, for instance? Why can't they meet dangerous foes and learn new abilities? Why should that be restricted to Naruto, Sasuke and whichever new character Kishimoto makes up?
Oh, and lastly: an arc with Jiraiya and Naruto's travels. Do it. The places they went, the training they had (although I wonder if they had any training, Naruto neither learned anything new nor grew up) and so on. There is unlimited potential in that. I'm surprised there aren't more awful fanfics about that.
