I prefer to keep the NA, NL, and AA as separate leagues. Then in 1901 move the teams to MLB that is NL and AL. This keeps your pre-1900 players on separate leaderboards from post 1900 players. The history still remains when you delete the league.
I don't think 13 has a problem with adding a subleague like previous versions did. If you want to have a draft say for the AL you could create a league for them let them do the draft then move the teams over to your league.
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