What if instead of having all these leagues across multiple nations, everyone was just in one big pool?
This way you can have players from micro-nations compete against other teams closer to their own rank, instead of a league full of bots. This would also place new players at a fair starting point against other new players across the globe, instead of being stuck at the bottom of a D4 league against active players that have been playing for multiple seasons. Whenever a new player signs up, give them a team in the bottom division of this global league, instead of throwing them into D3 or D4 just because someone went inactive or was banned.
Add every nation into the game, and then have the draftees of the different leagues be from the nations within that league. For example, if the nations in League III.3 are only Canada, USA, Jamaica, and China, then the draftees will only have those nationalities. An alternative is to randomize all of the nationalities for all of the draftees in the game.
You can keep the National Tournament, but have the micronations grouped into Regional Tournaments. For example, all players from El Salvador, Nicaragua, Guatemala, Honduras would be in a Regional Tournament, but would represent their own nation with their flag.
Keep national teams the way they are initially. Consider merging micronations into regional teams to compete against the rest of the world.
Because the main leagues would essentially be BuzzerBeater's Best, an alternative is necessary. I have no clue what kind of tournament you could substitute it with. Possibly the best players from each continent could be invited, instead of the best from each country.
Lastly, the free supporter would go to the champion of League I.1, since there would be no BuzzerBeater's Best.
This has probably been discussed before. I dont know how difficult this would be to implement or if the community would be in favor of this, but just wanted to throw this out there.