Fair enough, though in THAT character's case, she's full prosthetic (depending on the mythos of course, SAC is different than the original movie/manga, and probably different than latest anime too). She can be whatever (outward) race she wants to be.
Not to say your point isn't true. As you said, the Cloud Atlas weirdness.
Ghost in the Shell will always be somewhat problematic because a lot of the ideas that the series works off of - the concept of privacy, national and personal identity, culture, etc - are very much rooted in the Japanese perspective, rather than a Western perspective. However, given how few major roles, and even minor roles, go to Asian actors in Hollywood, and given how frequently Asian characters are either changed to Caucasian, minimalized, omitted, and worse, played by white actors in "yellowface", it's pretty glaring that the definitive piece of Japanese cyberpunk, with strong female protagonist Motoko Kusanagi, is cast using a white woman. If the movie was in a non-specific setting and the character was adapted to be, for example, Mathilda Kozinsky or something, it wouldn't be as much of a slap in the face.
Another glaring example was the movie '21', based off the book 'Bringing Down The House', which was about the MIT blackjack team that used their math genius to take the casinos for a fortune. The team was largely made up of Asian or Middle Eastern males, especially since they could pass for the spendthrift children of a Japanese executive or oil sheikh*, whereas a white kid with a $2 million bankroll would have gotten a lot of notice. The movie made all but one of the characters white, and made the token Asian a goofy kleptomaniac instead of a math whiz.