It is a breath of fresh air for anime to show the differently-abled in another light, without fetishizing the condition like most anime and manga do nowadays.
Ghost in the Shell is hardly the 'smoking gun' that proves that anime/video game adaptations will always suck unless they're Rurouni Kenshin good. They managed to get the visuals, sounds, and the themes right. They just missed the train on the story department....something that made the original a classic in the first place.