The highest skill of samurai in combat was actually horse archery. Samurai were respected leaders. They were the noble class of Japan. The side game for Samurai seems like it should be political, governing territory. Perhaps you're given responsibility for some daimyo that are unhappy with the status quo, and have to pacify the area. Seems like they could give you a minor noble type background like Ezio had, but make actually doing your job a more significant part of the game. Have the portuguese/dutch traders be the templars?