Yeah, not many black people in Japan. And it wouldn't surprise me if the Sevii Islands people were supposed to reflect Okinawans. (EDIT: apparently, the Sevii Islands are based on the IZU Islands south of Tokyo harbor)
But really, the lack of black people in a Japanese game can't be considered racist. The people just reflect the regions that they are based off of. The pokemon regions are meant to represent different areas in Japan. Kanto is similar to the actual Kanto Area of Japan, aka Tokyo; even the geography is similar. Johto is based off of the Kansai area (Kyoto, Osaka, Kobe, Nara), with Mt. Silver standing between them based off of Mt. Fuji, which actually stands about halfway between the Kanto and Kansai regions. Hoenn is based off of the island of Kyushu, and Sinnoh is based off of the island of Hokkaido. (That would mean that Gen V will likely be based off of Shikoku!)