It's not just that he's black, it's that he's a samurai in a game that's supposed to be about assassins. Putting yosuke in required them to rework a lot of things, since they suddenly need to allow players to play through the game as a guy that cant climb buildings. It required them to rewrite things, it was a lot of work for something nobody wanted. AAA games are very complex and a lot of people have to coordinate. You want to have everything on lock early so everyone knows what the final product will be, and what their part of it is. Adding in anything should be done sparingly as it requires you to tell hundreds of people things are changing and that they have new marching orders.
Delaying a game for 2 years only to make it less fun is just peak retardation. I can't wrap my head around how anyone thought floyd was so important youre willing to derail such a massive project. It's one thing if you tell a small team to make a "nigger samurai slaughtering nips" DLC or side game, but the main game? Utter lunacy. They could show him once in a quest, then let the DLC team cook up a yasuke DLC, just to keep the development pipeline intact. Or they could've made their male assassin a black dude, toss in some cutscene explaining why a black dude is in japan, and then just keep the rest of the game the same.