The second movie was great, but you really need to be into Ghost in the Shell to appreciate it, I think. It's more of a device for a philosophical discussion than a typical movie. As for the TV show . . . some of the best stuff ever put onto the small screen.
As to the main subject, they are really two different technologies with a similar purpose. The brain uses chemical reactions in addition to electricity, whereas the computer uses magnetism in addition to electricity. Further, whereas the computer has evolved around the
von Neumann architecture, the brain has evolved, in a more literal sense, in a manner we're still trying to figure it out. While it might be very possible to create a facade that appears similar to Linux or Windows, that would mask the tremendous differences in the underlying interactions. For instance, how would an OS operate in a system that lacked a CPU?