"Why doesn't Japan conform to American ideas of race?"
What you're doing is considered being ethnocentric, which is ignoring the culture that somebody or something comes from in favor of your own culture. While I'm not going to say it's racist, because I'm not some crazy social justice type, I will say it is ignorant of broader cultural issues. Japan is a country that is racially homogeneous due to their policies of isolation through much of history. People who under the American categorization of race are considered black generally don't live in Japan, except for a few there for business reasons (since Japan is one of the technological centers of the world).
It is not at all racist for a country's cultural exports to reflect their own people and culture. Not every country is the United States.
Interesting to note is the Game Freak added more people of darker skin color to the games with the Unova region, which is a representation of the United States (New York to be specific). Here we see an example of a group of people respecting another culture by depicting the racial groups of that culture within a game about that culture.
Sidenote: The people who in the United States are racially categorized as Asian fall into a pretty hilarious spot. They're "white" when people want to call them racist or privileged. It's sort of like Arabs, who for quite a good chunk of time were considered "white" under our classification system until 9/11 happened and all that changed.