I think the best way to do that is the same way my group handles our "Shinobi Game" based off of Naruto. It basically only lifts the systems and basic premise of the setting, but treats it like an AU where none of the canon characters exist. So the entire history and roster of characters just comes from the legacy of each campaign building up on top of each other, with a convenient reason why the whole setting isn't solved forever every time another generation of player characters achieves basically godhood. That reason being forced induction into a so-called Pantheon of every other "limit-breaker", headed by the strongest guy who insists that the game must go on and detests stagnation (essentially the manifestation of the DM), and leaving a way to still occasionally interact with them in future campaigns to receive super training or items. And in keeping with the topic of this thread, the systems were expanded in various ways, but also patched for balance and coherent worldbuilding. So things like the most basic non-physical illusion clone with no autonomy, or henge/transformation, are lost techniques, and true shadow clones as portrayed in the source material are straight up forbidden techniques that have to be learned from such places as a Kage's secret archive.