It is there, buried in the action and the aesthetics. It is an afterthought and doesn't go into much dept. Mystery is mistaken for dept. But that is a regular trope in Japanese sci-fi. So is blending mystecism with sci-fi.
Don't get me wrong. It is great piece of art to look at, but you do not have much to mull over after.
Then you clearly did not understand the movie. The movie is literally all about the main character trying to figure out if she is really a person, or if she is just another shell.
This is why the movie has
a very long scene in the middle FULL of symbolism, where the main character gazes at mannequins in a window, and spots a woman in an office who looks identical to her. This scene also has several close ups of garbage floating in the water, which is again symbolic for the feeling of self worth that the main character struggles with. And the climax of the movie is all about the central question of personhood. It is not mere afterthought that the movie ends with a climactic battle between an arachnid-robot and a human, and the mech fires shots that destroy fossils on the wall, and
destroys an image of the tree of life, but ending just short of man-kind on said tree. The message of the movie is pretty obvious.
It's literally all there right from the opening in which the main character is born. The way she
rises from the fluid is later mirrored in a scene where she goes diving, and
rises to meet her own reflection. And it is not mere aesthetics that we see her in the
fetus position during the opening either.
The movie is all about what makes us human. Are we human because we have a unique face, unique voice, unique memories, and because people treat us as a fellow human? If not, then what does make the difference between a human and a cyborg? This is explained in
this scene. The movie also has a heavy theme of reflections. We often see the Major gazing at her own reflection, especially during scene in which the afore mentioned aspects of being human are questioned. For example,
in the scene when they interrogate the armed suspect whom they arrested after the big chase scene, and find out his memory has been wiped, and false memories have been implanted in him. It is not strange that the very next scene is of the Major diving, to meet her own reflection and get in touch with that intangible feeling of what makes her a person.
This leads us to the goal of the antagonist, the Puppetmaster; To become something new.. something greater than a mere cyborg, and to merge with the main character. And this central question is literally woven into countless scenes throughout the movie. It is not mere aesthetics or directionless Japanese mysticism.
I think you just assumed the movie was shallow in its message, when it was in fact too complex for you to understand on an initial viewing. You are not alone. Many people don't understand the movie at first, because it is about a very complex topic that seems almost beyond the scope of just a mere animated movie. I didn't get the movie either the first time I saw it. It took me many viewings to fully understand the film.
And once you understand the film, you can start to try and figure out the ending. It is all about reflections...