Masamune Shirow has only had a few ideas in his entire writing career, and he keeps re-writing them.
If you take a look at Dominion Tank Police after having seen the later Ghost in the Shell stories, you will be struck by how much of Dominion seems like a rough draft for Ghost in the Shell.
Shirow also recycled some big philosophical themes. Apparently Shirow really believes that there is no non-physical human soul, and apparently he really believes a lot of outdated philosophy and science, so I can’t fault him for recycling big ideas. A big idea is much more important than a fictional franchise, and if you want to expound and expostulate your theory of a human mind as tabula rasa, you should feel free to do so in as many comic book series as it takes to get your idea out.
There are some minor details that get recycled too, with less philosophical impact. Batou’s external eye-goggles and the Major’s quest for a Beatrice-character who transcends the limits of the other characters – are both recycled versions of earlier details.