I feel that having people actually be characters from the Anime/Manga would only restrict the number of people who could play, after all there are only a certain amount of characters in the story. SO, I was thinking that players make their own ninja that is not part of the story and have them interact with the people from the story. For example, you could have Kabuto or Madara be raid bosses or something that the players kill to get rewards.
As far as rogue ninja go, i think that the players can be divided into 2 groups for pvp, those who belong to a village and the rogue ninja. To become a rogue ninja, there could be choices while on missions that will lower your reputation with your village and at a certain point the game will either force you to leave the village or it could give you the choice to. Or upon character creation you could choose rogue ninja. The division between village ninja and Rogue Ninja will allow for simpler pvp scenarios, such as Capture the Intelligence. As far as PvE goes, obviously village ninja will get missions from their respective hokage, Rogue Ninja can get their missions from influential rogue ninja from their respective villages that they left. For example, a Konoha rougue ninja can get their missions from Itachi or Sasuke.
When creating their character, i believe that players should be able to choose their desired village, which will decided their primary chakra, however upon character creation , have a personality quiz to decided a players secondary chakra type. This way, players are made to the individual which could add depth to the game.
When choosing whether to be a rogue ninja or village ninja, 2 ideas come to mind.
1) you can have players upon character creation can check a box or click a box that will cause their character to be a rogue ninja from the village of their choice.
2) having a choice after reaching a certain level to become a rogue ninja. This way it gives players from a village a feeling of revenge during pvp against players who are rogue ninja, adding some depth to the game.
These are just some ideas i've picked up from various other successful MMOs. I just adapted them to fit into the over all design of Naruto Shadows. I feel that these ideas would open up the game to a lot more people and really make the game have that MMO feel to it. I hope that this helps or gives you ideas.