Just imagine it; assassin meets samurai and the ninja. The thought alone calls home a multitude of possibilities for character designs, besides isn't Ubisoft's Assassin's Creed assassin nothing more than a ninja in a cool jacket?
Feudal Japan is filled with civil wars and alliances that would be a perfect fit for the Assassin's Creed style. It could also lead to new fighting styles and assassin weapons; just think about what the franchise could do to classic Japanese weapons like the kunai or suntetsu. Plus, being in Japan means amazing roof running evasions and killer ninja smokescreens.
Even if Ubisoft didn't want to go with typical ninja style, there is always the option of going the route of Imperials versus Shoguns, which could easily adapt to the Templar versus Assassin story line.