Akatsuki Member Usage
Now Kishimoto made the Akatsuki a pretty great group. Characters like these are what makes Naruto good IMO. But that said, Kishi can't fit everybody's taste. I'm fine with Deidara and Sasori's role, but I wish Hidan would have been put to better use. Like said in another thread, I think it would have been cool if these important ninja started getting killed everywhere and nobody knew what it was from. Thus countries started blaming each other! But in reality.. it was all Hidan's doing. With blood samples, he killed them from afar with his curse. Shikamaru ends up leading the deaths to this situation and it basically becomes the same situation leading to Asuma's death. As for the second encounter, I probably would have tried for a better fight. All these characters were in the battle just to be ignored, which didn't flow well with me

I don't have as much feud with the other members. Although I would make it clear that sick Itachi was around Sasuke's level but would have killed him with Susano'o if he had wanted. This "power gap speculation" is unneeded~
Danzo
I know a lot of people hate Danzo but I love the role he plays. Other members have probably seen me say this before, but I wished that Danzo would have escaped the Kage summit and successfully went into hiding afterwards. He would command Root from the shadows and lead Konoha from the inside. Meanwhile, the K11 would get into fights with Root members along the way leading to more panel time. Eventually, Tobi would finally find Danzo and have Sasuke fight him, leading to a repeat of what happened in the manga.
The Ones Who Know Everything
These Hashirama flashbacks ARE great but I feel like TOWKE could have been used differently. Just get the flashbacks elsewhere! Now what I would do with them? I never really had a clear idea of who it would be, but over time I thought "why not let the Sage have a daughter who resented him for not giving her a chance to succeed him"? She would be.. you guessed it, an Uzumaki. She would also lay her conscious in a special shrine laid dormant until somebody awoken it. Orochimaru would do this with Sasuke's help, and thus the truth would be revealed.
TOWKE would talk about how the Sage secretly knew that the world was doomed to be in eternal chaos but put his last faith in his sons to do what he couldn't. The idea behind this would be to show that even the "god" of this series believes that the world is full of evil. If the truth comes from such an authority figure, it makes it almost seem like a fact. Only a handful of people will hear these words: Madara, Obito, Orochimaru, Sasuke, and eventually Naruto. Madara will be the first to uncover the secrets with the Rinnegan, and this is where he starts his plan for Infinite Tsukuyomi. He found a loophole in the Sage's logic: they don't have to fix this world, just make a new one. Then he will pass on the word to Obito, which would help everybody understand why he is the way he is.
Orochimaru and Sasuke will then hear it at the same time. Orochimaru just wishes to surpass the Sage in every way possible, so he's sworn to eternal life in order to contradict his teachings. Sasuke sees everybody's life as brittle and fragile, believing that the Elder Son should be given a shot at his attempt for world peace (I'm still iffy on Sasuke's outlook). And finally Naruto, who will of course go against authority's word and promise that the world still has potential.
There are other things like relationships I would develop but these are more major for now.