I agree, those teams you listed are closer and may make for better rivalries.
But the affiliate world is a cut throat business. Much like the big leagues, if you don't have a state of the art stadium that's less than 10 years old, you better be working on getting one. Unless you have a really old stadium that has a rich history like a Fenway or Wrigley.
Some teams get a new affiliate almost yearly. The Nashville Sounds have had a bunch just within the last 10 years. Of course they have an old run down stadium that will probably cause their death after this year.
Then again you could be like most of the Braves farm clubs, and name your team the Rome Braves, Richmond Braves, etc. So when the team changes affiliation you have to change your team name.