After ten minutes of watching this film I at one point thought to myself, "I have no clue what is going on". I was able to catch on to some of the most basic points, but I had no idea why the characters were doing some of the things they did.
Something I did however note was the depiction of Motoko Kusanagi. One might assume her being the lead in such a film, that her character might be less subject to the male gaze, but within the first few minutes of the film she strips her suit away and is naked. Other characters are able to use their thermpotic camouflage but are able to do so without taking their clothes off. It seemed redundant anyway considering she did not have any genitalia.
I believe that the biggest theme of the film asks the question of whether or not our memories define us as humans and shape us (Interspersed with the idea that technology is increasingly "taking over" our lives and what that overlap might be). The best answer is that which is thinking and feeling (<--perhaps the most important)with cognitive deduction of right and wrong is human.