>>720629194
>>720628975
>Ainu 
I thought that was supposed to be the central conflict of this game, the expansion of the shogunate's rule into Hokkaido, the Ainu's lands where before they were more or less independent (and did their own sorts of diplomacy with China, Korea and others, similar to the Ryukyuans who were also incorporated into main Shogunate / Empire). The bigger thing that made me wonder is that apparently except for a single optional outfit, the protag does not seem to have any cultural Ainu signifiers - they could have had her playing their stringed instrument instead of a shamisen, they could have put her mask or robes in Ainu style, they could have given her one of the distinctive lip tattoos that women had, but it doesn't seem to the protag has any of those things. 
As far as controversy, I didn't think "Shogunate comes in and takes over, suppresses independence etc" was some sort of big no-no as historically that's what happened - the Matsumae were given control of that domain and basically used subjugated the local people to benefit the daimyo / shogunate, and later empire. As I recall the daimyo basically came in and said 
>Oh yeah, all those silk robes your leaders got from trading with Qing China? Yeah give em up. 
and then went to the Shogun and was like
>Look, we in Matsumae domain have access to the BEST fancy silk! Its our super special exclusive thing, we'll keep it flowing as long as you make sure that we are in power to keep the natives in line. 
So I'm not sure what would be controversial about a colonization story; the question of accuracy or what form it took at the time the game is set is one thing, but I didn't think the idea was particularly in debate.