Spoilers included by necessity:
I found it really disappointig that the final solutions to the main mysteries didn't actually have anything to do with the technology of GITS's world like would have expected. Why not explore the chance that, for example, the EXACT replicability of things electronic input/output to brain allows could result in different minds processing the raw thoughts to a same conclusion as the results of human minds being at some level identical? Instead the "copies without original" were explained through memetics, despite the fact that the concept of memes doesn't have much to do with random people deciding to do the same thing randomly after witnessing some event.
This reminds me much about the reasons why I don't like Paranoia Agent - making a work that involves psychological and sociological dynamics, but then exaggerating the phenomenon to totally unplausible levels causes it to not deliver any real message, or illustrate the workings of these theories in educational sense. Some may find it brilliancy, but I find it as a lacking sense of reality and/or poor grasp of the concepts it is all about. It's even more frustrating when it's offered as a solution to a mystery the whole series is based upon.
Also, what's up with the Major's outfit? Nobody wears clothes like that, that's pure fanservice. It's up to you to decide whether or not this cheapens the work (GITS is not a character-driven show to begin with after all), as long as you aren't a hypocrite and think that in the case of Code Geass it does but in the case of Ghost in the Shell doesn't.
Some praise the difficulty of the plot to follow, such as mentioning a important, relating case in one episode in the beginning when one has not a clue of the whole picture of what the series is about, and then casually referring to it later on. I can't see how this is a positive thing and somehow adding 'depth' into it and not different from just bad storytelling.
My strong opinion is, mindfuck for the sake of it is never good, it should be used only as a tool to serve a purpose, to deliver the message of the work if it cannot be effectively delivered any other way (such as in Paprika, in which it is fun to guess whether what's happening is a dream or real event, or to a lesser extent in Serial Experiments Lain, which uses uncertainty and inconsistency as a metaphor for the layman's defective understanding of the nature of modern technology and detachedness from the world's clockwork functions).
Overall, Ghost in the Shell Stand Alone Complex is pretty average and unrealistic cyberpunk that has nothing that is actually worth a honest thought of 'what if this happened in reality' and you haven't seen somewhere else already. And by this I mean most of the Stand Alone episodes are based onto recycled cyberpunk ideas.
