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Minor league contracts:
Teams do this in real life, to stay under the major league contract limit of 50 they will sign either depth players or prospects to minor league deals, this could help with contracts limits in the game.
Players that are fringe major league players would be less willing to sign these deals and may wait to sign them until later. Players from Europe, Asia, etc might also prefer to play in their home country over the minor league.
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Independent Minor Leagues:
Could be an option to make minor leagues semi-independent, this would mean that they could sign players to minor contracts, send down and call up players if there’s a different minor league bellow them and make their lines. They could be overrided by the major club.
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Relocating, Transferring and Affiliation Agreements:
Relocation of minor teams mid-game as well as relocation of teams in general would be a great addition to the game and I think transferring or swapping minor league teams could be a good addition too. Minor league teams change affiliations between teams and relocate a lot in real life. These should probably only be for the player to decide though.
Affiliation agreements are more a longshot but I think could work, a minor teams willingness to sign an affiliation could be reliant on a number of things. You could negotiate many minor contracts the team could give out, proximity (to major and other affiliated minor league teams), how good your minor teams have done in the past, how good they’ve done under you, how good they’ve been while affiliated with other teams (worse teams are easier to get an agreement with), and if they get a “no-relocation clause” or a say in where they get relocated to.
(Should be able to turn all of these on of off in settings if they were implemented IMO)