Oops. Forgot to mention that I was referring specifically to GITS. I haven't bothered to see RahXephon.
GITS is difficult to wrap your mind around. Especially when they are talking about things that involve accessing the internet with just your brain, cyber-technology, and the concept behind "ghosts". There are individual episodes that break down these concepts to feed you bit-by-bit what you need to know, then suddenly, past and future episodes suddenly make sense.