The fact that Yasuke, of all people, someone who’s been featured in so many different kinds of media, is the straw that broke the camel’s back is just incredible.
The game isn't getting crap from Yasuke being the main character. It's getting crap from the blatant disregard of the Japanese culture on dozens, perhaps hundreds of points. The list is enormous, but here's what I got from the top of my head:
1 - Ubisoft claiming Yasuke was a "legendary samurai" and a Japanese historical icon, when in reality there are 3 paragraphs written about Yasuke. The Japanese find this a bit insulting and revisionist, as there are contemporary historical people who have a hundred times more historical records about them.
2 - Ubisoft mixing up stuff from different seasons (which bear a lot of relevance in Japanese culture), like putting grain harvest from Fall next to blooming sakura from the Winter.
3 - Stealing artwork from Japanese creators like a sword from the One Piece manga, banners from Japanese larpers, lanterns from temples without permission, figurines, etc. The list here has dozens of examples.
4 - Ubisoft putting Torii arcs as entrance to random villages, whereas
the Torii were used as an entrance to Shinto temples.
5 - Ubisoft putting burning incense in an outdoors Shinto shrine, when incense is only used inside Buddhist temples.
6 - Ubisoft putting the tatami placements wrong, in an audience where the samurai are sitting in the wrong formation and posture, in front of a daimyio who would probably kill them for it.
7 - Naoe supposedly being the furtive character walking around in the middle of a village wearing a sword on her back, which would immediately call out all attention towards her.
8 - Yasuke walking around wearing full body armor, which was only used for battle and would reallistically send villagers either running away like hell at his sight or attack him in defense.
There are many more and some Japanese are apparently gathering up all the evidence to present to the government. What the government will do about it, is up to anyone's guess.
Most of these may seem irrelevant for westerners, but they're really important to the Japanese culture, much more than one of the main characters being black and LGBTQ.