>>33178460My headcanon is that in most regions, there's a civilian legislature (typically with one representative elected from each major settlement) and judiciary. The league Champion, Elite 4, and to a lesser extent local gym leaders act as the executors of the laws. This stems from the Pokemon Champion traditionally being the leaders of regions until modern reforms.
Because Kanto and Johto share a league, they are technically a single political body, known on paper as the Kan-Joh Union. The legislature meets in a federal district taking up a small part of Saffron City, while the union's highest court is located in Goldenrod.