In thinking (again) about this movie, another peice of interpretation's sprung up. I'll use three of the more striking and disturbing peices of imagry from the movie as examples: the assasination in the beginning, the fight against the tank towards the end (where the main character wrecks her body), and the very end where she wakes up in a child's body.
Motoko's filled with the existential dillema of recognizing herself as a peice of machinery in a vast system she has no control over (she's an agent in a CIA-like law enforcement agency dealing with technology crime). She's doubly entrapped: both in her role in society and the fact that her body is essentially property of the state.
I think she also feels a strange sort of alienation, being that her societial function exempts her from normal rules. Think of the assasination she carries out at the beginning. The rationale for it is explained from the state's perspective, but from the human perspective its still just a senseless killing. These pressures seem to weigh on her as she wakes up the next morning: she's done something that should be censured by the ethical laws of human interaction; but is sanctioned because of the action's importance to the state. In other words, she's very literally a tiny machine in service of a greater one, and she's afflicted by bending her intelligence to it.
I think the "ghost in the shell" metaphore can be applied at two levels: the human intelligence inside the machine that is the body, and the human intelligence inside the machine which is the emergent result of human interaction, eg: the state and the economy.
The second image: the fight with the tank. As the tank is spraying bullets at her, the shots run up the wall (in what seems to be an abandoned train station or museum), and they trace up what seems to be the tree of life/evolution, destroying all of it up to the last entry: Hominis. She strips to her camoflauge layer (which also seems to be her skin), and jumps atop the tank. In what seems to be a desperate and totally senseless act, she tries to rip the hatch open with her hands. You see her artificial muscles buldge and stretch accross her shoulders and back, then tear and snap underneather her skin, then through her skin, and she falls broken to the floor.
Why such macabre and wasted effort? Surely she could see that she was destroying herself without hope of success; but she does it anyway. That, I think, is the depth of her desparation with the role she fills. She hates being a cog, and she hates the shell that enables her to be it. The self destruction is a result both of her passionate desire to be autonomous and exert her own will on the world, and of her hoplessness to acheive such freedom.
Lastly: while her body is shattered she has a conversation with the "puppetmaster," which is a conciousness that has emerged out of the complexities of human interaction. It offers her the opportunity to "merge" with it; to become the same conciousness. Its benefit, it explains, is that it needs an element of mental diversity, or it will become stiff and overcome with its own inner complexity and die. The benefit to her is allowing her to exist on the same plane of existence as it, the suprahuman level.
She wakes up, and finds herself in a child's body. I think there's an interesting connection with the corinthians verse used earlier in the movie: " When I was a child, I spoke like a child, I reasoned like a child. Now that I am grown, I think like an adult. For now I see as though through a glass, darkly. Then I will know fully, even as I am fully known." (paraphrazed, I think that captures the important ideas and I don't feel like looking it up).
The quote implies that there's an analogy between how children and adults think, and between how adults and... whatever's next (gods? angels? transhumans?) think. She attains this next level of mental capacity via merging with the puppetmaster, and again sees the world through the eyes of a child.
And that, friends, I see as an alegory for all of our lives.