To be honest I want to say ditch the villages. Go post apocalypse. We already have the apocalyptic weather. Lets have the villages destroyed, maybe as the end result to the current plot written going awry. Then spark the creation of organizations/gangs. I wanna say move the time setting from the nomad era to a more modern civilization. Im thinking a destroyed city like setting and wastelands. Now I don't mean to bring in guns and cars, but just something a bit more modern. A lot of this is coming from the inspiration of Fallout: New Vegas by the way. Some organizations are good, some are bad, and some are just neutral. Which one people end up in depends on themselves and where they go IC. Have a standard starting point in a neutral area for everyone just starting, and a set organized map where you can't access one area without going through another. Traveling post should also be more than one post entering and one post exiting. Some time needs to be spent in areas and interactions need to be made with other people.
Now organizations/gangs should be registered and should be detailed with the approval of admins. The number of them should also be set to fit the number of members we have. Each having a member cap and territory. Oh and clans can be dispersed about the lands. No longer tied to a village they're free to go where they please. Bijuu should roam again and be random phenomenons.
Anyways Im done with my rant. Thats just what I think would really set this apart from the tradition naruto rpgs.