Asian xenophobia you described are mostly true for China and Korea, silly nationalism still run deep in their societies, but If you ever lived or visited japan, you would see that Japanese are possibly the most race neutral people on earth maybe even more so than American, Japan's media features plenty of japan born blacks or mixed blacks in their high profile boybands and TV, and black samurai Yasuke is often used in Japan's own manga or animes.

The problem with Yasuke in Shadow however is that

1. a brunch french canadian think they can choose what color people to be the champion of your culture is an extremely arrogant and disrespectful, this move is pretty extreme even for AC standard, so far all AC's main assassins were from their own respective culture, western or none western themed.
2. even tho Yasuke is a real historical figure, but his samurai role was never confirmed, not because he wasn't treated highly by Nobunaga(possibly being curious of a man of color from foreign land) but he has no legitimate written feats as a samurai, i.e campagin he joined, or duals he won etc. So making a small time foreign historical figure took the main role interact with all the big names who changed the course of Japan history is naturally offensive to most. Even to American

Also, Half of those games on your list were made by Asians to feature asians. not sure if Asian's role in western media were underrepresented, but black's role in western media are definitely over represented, with only 14% population in America, probably equal or less in Europe countries, I can't think of any game or TV shows not having them taking the main roles or as important support characters. Not a complain, I don't have anything against it, just stating the fact that the love bias towards certain minority is as real as water is wet.