Frankly speaking, there is one easy way to go about it.
Usually to gain the nationality of a certain country, you'd need to live in the country for a certain period of time. Using that, nationality change can be given to players who:
- moved to the country at 18-19 years old.
- has been in that country for more than 10 seasons.
- has never played for the U21 or senior NT.
This would somewhat benefit the senior NT of micronations (they'd stand a chance to get a good NT player who wouldn't qualify for their home country and be more competitive), and not at the expense of the bigger countries (since if he has never played for the U21 or senior NT by the time he's 28, it's highly unlikely that he'd be given a chance in the future anyway).