As it is now when you want add a minor league the game will create a league that mirrors the size and structure of the major league. Editing the structure of the league to the size and configuration you want is easy enough if you know what you're doing but how about this....
When you create a new minor league have the ability to specify the size and structure. Have an option to mirror the major league, or for a custom structure and have the ability to manually affiliate the teams to the major league parent.
Whaddya say developers, am I asking too much?
