Ghost in the Shell paints a world view very subtly at times. Motoko isn't so much singled out rediculously in her series, it's a reflection of a larger picture. When an economy/nation is doing well, skirts get shorter. This has been documented in the U.S. for the past 100 years. Japan is toying with being a super power in the first season of Ghost in the Shell due to the research of the past national trials (nuclear warfare, aging population) coming to fruition. In the second and on through the movies, the refugee situation and the northern provinces bring the country back down. Now notice how in the first season, the prime minister is wearing exactly what a female politician would wear in a socially conservative country- it's nearly old fashioned (i.e. reminiscent of the late 1980s in the late 2120s), it's blatantly red (research has been done about red clothing and power/authority assessment), it's distinctly professional attire, it's unmistakably feminine...but it also has a slit in the skirt nearly past the waist. As the story goes on, the same character wears nearly the same thing in nearly the same setting but due to the state of the country the slit is much lower.
In any other series, I'd throw that assessment away. In Ghost in the Shell, they actually rely on little details like that for world building.
As for the primary entreat of this thread, over-sexualization...The Major is actually under-sexualized in a way. As first created, the character is homosexual. The only times the show's pointed to her being sexually involved or even interested was a)when she hangs out with the lesbian couple she's a semi-third wheel to b)when she jokes in the second season about taking the team to a gentleman's club c)when she calls a teenager on his bluff. (The character in season two wasn't a sexual relationship, as everything from the relationship starting when they were children to her own definition of it being purely emotional.) And that's kind of the point: the character is a brain/personality piloting her artificial, swappable body. The fact that it's designed to look like a common civilian model, that she doesn't pursue relationships due to lacking some of the biological components that drive it along with a pseudo military career and background, that she doesn't feel what happens to her body she pilots it...all this leads up to one of her big character points and a plot point of the series as a whole.
A lot of what Ghost in the Shell is about is how human Motoko Katsuragi is and what being human in the first place means. Her under-sexualization is part of that. Nearly every attempt at fan-service is portrayed in a much more detached, clinical manner. The first movie opens with what should be pandering nudity, but it's technically PG-13 because it's artificial(i.e. like a background painting or sculpture) and medical(i.e. like surgery). The language in the movie drives it closer to R than the nudity in...well, that scene. When the character is shown exerting her body, it's blatantly from an engineering standpoint-like the time she ripped her muscles trying to pry a tank hatch off. When she's in deep feeling, it's from swimming the internet.
Motoko Katsuragi is one the least sexualized characters. And, at least I feel, that a lot of Ghost in the Shell is lost on the audience that doesn't understand that.
