Itachi's story would be interesting. But you'd need to create the world
Also, you could make... let's see....
What if Hiruzen died on the 3rd war and Danzou took over?
What if Naruto and peers were trained under him?
Erm...
That ok?
Or what if Naruto & peers graduated earlier because of the massacre? (you know, it killed a bunch of ninjas. Replacement would happen)
Including darker themes would give the story a nice touch. Drugs, because ninjas are always under extreme pressure. Politics, because corruption should be there as well. Slavery, because why not? Dirty Missions(assassinate people to sell protection, things like that)
Don't write a Mary Sue, be careful with important character being one dimensional and...
don't make Naruto need explaining multiple times!
This would be fine in the format of a manga or anime, but don't do this on a fiction. Having to read the same thing repeatedly is incredibly annoying for the reader. Make him stupid in another way... like clumsy
Reading the same thing multiple times makes me want to punch the monitor. Kishimoto does that because he's explaining things to kids, you really don't have to do the same...
Readers should see the emotional development of the characters. Writing about the main character doing everything without even thinking twice about it is a bit too much.
That, of course, is about Naruto.
Since you didn't exactly specify...