If my system had always been used, there would not be any isolated teams, except in unusual circumstances, such as when a lot of new owners join in a burst, and then there is a slow decline in teams for a country. In cases like this, after 5 or 6 weeks, many of the new signups will have stopped logging in, and you will have leagues with just a few active teams.
But that happen in BB several times, one time with the travia action, then with the banner at hattrick and again with the news that they are in the exchange programm with ht.
This can be better be handled by how new teams are added. When there is a burst of new owners, you can simply fill as many leagues are needed. Then in the slow periods you can be more selective. Even in the slow periods, BB is adding lots of owners - but are losing a lot more. They might add 50 new owners, while losing 100 owners. Right now they try to maintain IV.1 with 16 owners. In fact, if IV.1 loses an owner during the bot'ification on Monday morning, the team will often have a new owner that same day. Meanwhile IV.40 may be losing owners for weeks, before BB gets around to replacing them, perhaps during the next signup burst.
But instead, you could add teams to the leagues that have the most openings. You might have periods where leagues have around 12 active teams, some with more, some with less. But that is better than having the same number of teams, but with some in leagues with 16 active teams, and others in leagues with 2 or 3 teams.