I propose we merge micronations if following way: Make top divison shared, keep lower divisions national.
+1000.
My honest opinion is that this simply isn't an issue that can be fixed easily and really is difficult to envision a fair and proper solution absent a reboot of the entire game world, which is entirely unpractical, or a new parallel game world, which is mostly unpractical and a lot of work for development staff.
I think if that if something were to be done, though, a continental SuperLeague structure is probably the way to go. Not just for the micros, though it would give them something to aim for, but for every continent. Heck, maybe even a World SuperDuperLeague made up of champions of the continental leagues as well.
There are a metric ton of balancing issues and mechanical issues regarding promotion and relegation of the different nationalities that would need to be fixed; it's easy to have 1 team promote from each of four national leagues, for example, but if three of the four teams demoting are from country A, they can't all go back easily to the national league.
Still, I think of the ideas I've seen now that I let myself read this, I personally like yours the best.