I wanted to suggest some combat models that might help for developing the non-jutsu part of combat.

Although I'd first like to say, the current hand-sign system is EXACTLY what I was thinking would work for a naruto game. Really amazing. It could use some more interface, like showing the handsigns and names in icons, I guess like in a rpg spell/skill bar at the bottom. Eventually a personal Jutsu book. I was also thinking of a chakra usage chooser, likely like those mini-golf games that bounce a line back and forth along a meter and you have to time it to choose the right amount of force (chakra). Maybe one for where to distribute the chakra (top = head, mid-arms, bottom = legs). With training, it becomes more accurate or within a smaller range.

Now back to the Non-Jutsu Combat Models, some of best ones I've found so far are:
- Pirates, Vikings, & Knights 2 : Available as a free Source mod on Steam. Easy fighting, blocking, and projectiles. Very functional and easy to use.
- Lugaru: Available as a free demo, with the source code for the full game freely available. This was the original model I thought would be good for a ninja game, as it's already ninja humanoid rabbits. The combat speed is a little too fast though, so maybe a way to control combat speed, or maybe combat speed increases with training in ShinobiLifeOnline?
- Infinity Online: A game that has since disappeared (Only trace: http://www.gameborder.net/game/infinity-online ). It had a very interesting combo system using both mouse buttons and a couple of other keys in various and even redundant combinations, including 2+ buttons at once (would need a very forgiving algorithm). The numerous fighting combos just flowed smoothly and elegantly into one another, unlike nearly all other hack n slash games that have chunky animations.

I do have other examples in mind, but the combat systems are not very good or precise or reasonable to use.

P.S. I do hope custom control setups will be implemented at one point because the current way to run is quite ridiculous and aloof. I would say something much closer to the common FPS controls would work better.