No nationality, race, or culture is a monolith. I'm not Japanese, but I have the same concerns as Japanese critics I've read who don't like the imperialist message of the narrative. The fact that it was well received by Japanese game critics doesn't invalid this critique in any way.
I am a historian by background, and very much opposed to the official telling of history that often prevails in pretty much any nation state focusing on 'big men' and 'big events'. However, I don't see the way the story is portrayed as especially problimatic versus say most other big budget games. For instance, do you take the same issue with say AC games, with their distorting of all the periods they touch, historical figures, architecture not always true to the period, etc. What makes the message here particularly pro Imperialist? I mean samurai were very much revered in Japan historically, or at least accorded priviliged position. I am not arguing that was a good thing by the way. Just slightly baffled why historical sensitivity comes up particularly with regards to this game, particularly when Japanese developers also contain a lot of fairly distorted content about the West - and vice versa. At the time this game was based, the Mongols were also the vastly greater power, just a number of factors some induced by the Japanese, others seeming luck, resulted in the failure of their invasion.
Nocturne: I understand what you are saying and where you are coming from, and largely agree. I don't think the way you make your argument is going to bring those who don't to your perspective though. Of course, Wild Bill say was very influential in creating the skewed image of the Wild West. And Samuries and Knights did have their codes, but they also occupied priviliged positions in their respective societies, and peasants were continously subjegated manipulated and oppressed. People today are also kept in their place, even while not always being aware how that comes about, and that there is a great deal of continuity with the past. However, I think part of your criticism is a general one, and can be levelled at most games, which construct the hero figure, when in fact individuals mostly play a small (but important role) in changing society for the better. Most is done by collectives and a great deal of graft.