One glaring thing i noticed that people have missed is that Yasuke had no last name (family name). In ancient times, Japanese peasants didn't have last names only the nobility and the samurai did. So the fact that Yasuke has no last name/family name and was never given one means he was never accepted as a samurai. (besides the fact that you know....the title of samurai was passed down through blood and you couldn't just become one anyways)
Of course this is just if Yasuke did exist, but he didn't.
Even if he was a full samurai the reasons for making him the lead character are obvious and I’d still have a Japanese lead. If they were so hard pressed to include him they could’ve had him as someone you meet. Seems like a slam dunk to have a Japanese protagonist in a game like this