This sounds awesome, especially the part about determining your own missions. I also want to form my own village. Im interested in creating my own organisation and detailing each facet and department of it (these can be abstracted when not in use). Then determining goals and how to achive those.

I think that its a good move to remove some of the more powerful kekkei genkai, or at the very least ringfence them so that they exist as the top power tier, but arnt available to PCs. I think not having some of them would essentially de-fang the great villages but if they were too widespread then they'd be easy to learn.

Part of what interests me about Naruto is the possibility to create new ninja abilities. I dont know all of them because im still on shuppuden, but im more interested in creating than acquiring like some great eyeball quest. A long time ago i created 3 ninja for a poor village that had differing abilities, they were all really unique and i gave them to a GM i was co-gming with for a rival village squad. If you let me join you might see some of these. I suppose it also helps that i read a few books on ninjas aswell.

One thing i'd like to do in this game is not necessarily being evil, just independent, being calm and relaxed is much more conducive to success... and chakra control. I'll be employing my own philosophies for the organistion. However naturally i'm a team player and will work with my team to keep them happy.