Lets take storm 3 as a base.
1.Enlarge the map
2.Add travelling through trees.
3.Instead of a Naruto story, create an open RPG storyline
4.Real characters from Naruto would be NPC's
5.Story set 1 year after 4th war.
6.Make usage of Jutsu more interactive, and arsenals larger and customizable.
7.Battles have to become more strategic, including elemental weakness and advantages, depending on how you created your character(s).
8. Effective use of teammates by allowing you to create pre battle tactics, quickly changing them during the battle, and by creating an intelligent, but not overpowered AI.
9.Singleplayer only, seeing as how creating such a complicated battle system would be practically impossible in multiplayer with the current technology.
Basic battle system would be taken from Skyrim and improved on, greatly, to fit the Naruto universe.
It would require a completely new physics engine as well, due to different rule sets.
Obvious choice would be cell shaded graphics.
Anything beyond regular 3 tomoe sharingan would not be usable by Players, in fact limit the usage of KKG as much as possible.
Problem is how to deal with taijutsu and genjutsu. Seeing as how Ninjutsu and Fuinjutsu would be fairly easy to deal with.
Oh and of course, I would love if Fuinjutsu was explored in more depth, allowing a more unique approach to the game.