The idea of the X-Men as these grand overseers of the entire mutant race is an unstable one due to the series' conceptual idea of the X-Men being the underdogs and the outcasts, not the leaders of a kingdom. We've seen it done with Cyclops, and in-universe you can mark that up as a success or a failure, but that's really more of an Inhumans story. The X-Men aren't the type you want to be doing an Avengers World kinda story. Or maybe they are, depending on the run that they're in. The organization of the group should ultimately be dependent on the story. So come up with interesting conflicts and base the organization of the X-Men around that.