Something to throw out there, and this may not even be relevant, but I'll mention something I did.
I have a 24 team fictional, all teams based in USA. Some teams are in major centres, such as St. Louis, Baltimore, Pittsburgh, but I also have teams in Columbus, Boise, Shreveport - not exactly mega centres. What I did with my setup is, each ML team's affiliates are in the same state.
So I checked Wiki for city populations by state, then picked a city I felt could support a AAA Team, AA and A. I based it on my average attendance I wanted and not on real life populations. So for example, my avg attendance for single A is 2500, so I picked a city with a population of 20,000+. I don't know if that would work irl, but in my fictional world it does.
Anyway, I just wanted to mention this in case you're planning on having a few levels of minors. With 50 teams eventually, you'll want to keep some cities that can support the minor league teams.