In your opinion. Some Japanese devs said if there was a game set in Japan, then it would be be inaccurate to real ninja, since ninja don't do much assassination. And they also said that there are so much ninja/Japan games that it would be a bit unoriginal from their other locations.
I think that they can work around these problems. AC is known for making cool things happen while sticking to real events. Japan could be no exception. There could even be dual play, like you can switch during some segments to also play as a samurai and fight in wars. Both have access to different things. It would be like a Lego game... But actually good.
And the AC in China was all about stealth and killing... What about Japan? Y'now?