The relevance with Japan is that in AC2 (I think?), there was an assassin there. A lady I think. And her statue was in the shrine in the villa. Other than that, I don't see Japan having any other real relevance other than that tiny fact. The fact that it takes place in the american revolution makes more sense considering one of the subject 16 puzzles.
It had George Washington with the apple. So maybe he'll be the villian, as Borgia was in AC2 and Brotherhood?
edit: Guess I should've read ahead a little bit.