Would this be possible? I know in the show some ninjas can "Create" their own jutsu, would it be possible to allow clans to have a jutsu made for their clan? Or at least give them a special one for being in the clan or something? It would add an awesome dynamic to the game I think.

Ok I know you plan to have all the villages, and such. But in my opinion if you make clans enabled, you should have empty villages, in which clans could claim, and have their emblems show up on banners/flags. In which players can go back to have say vaults to store stuff.

How I think it could get set up.

Clans require 5 players.
Ability to claim a village, 10members.
Clans can fight over villages, doing sieges on villages.
If you have different type of ninjas; Medics, combat, etc. Allow them to have some they can "cloak" the village to hide it, which would require a ninja of equal to higher level, use a jutsu to "dispel" the cloaking, before they can siege/raid the village.
Have a online/ingame map, that updates the clan owned areas, so people can see if they are friendly, neutral, or evil.

I don't know what all you have planned, but you should make it able to do your hand signs while walking/running.