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Perhaps you could set them up as divisions within subleagues. Maybe along these lines:
SL1=MLB with American Division and National Division
SL2=Independent League with Pacific, AA, and International Divisions.
Set schedules to allow divisional play only and set up your playoffs however you want.
This would put all players in the same overall pool. It would not allow you to have different rules for each league. It would also not allow for different league financials unless you controlled the teams individually. Anyway, it's an idea.
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