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Rickey's system certainly had a revolutionary effect on the game, but every individual element of it had been tried fairly extensively before. For many years teams had experimented fairly extensively with owning farm clubs, although not on the scale Rickey did it, and everybody farmed out players either through optional assignment ior informal gentleman's agreements. Although fully owned farm clubs were not very common, major league teams often had close relationships with friendly independent minor league clubs, for example, Charlie Comiskey's White Sox with Milwaukee and San Francisco or John McGraw's with the Baltimore team run by his old player Jack Dunn. These can be thught of as independent minor league teams that had informal but real working agreements with major league clubs.
Major teams did not often sign amateur players and bring them all the way up through the minors until they were ready for prime time, but as long as you're using the standard historical database, those are not normally the first year players you're getting. What you get are players ready for their debut season in the major leagues, and if you have the draft turned off, what you get is essentially the player procurement program the real team actually had, whether that involved a farm system or players exclusively purchased from minor league teams. In the real world, going back to 1900 and even before, the major teams would not find a place for some of those players on their own rosters but they would not want to lose them, and so they would option them to a minor club or otherwise keep a string tied to them, as the expression went.
Considering all this, I believe that playing with a farm system, but with incomplete minors, is the method truest to the real situation of pre-Rickey major league clubs, and it's actual closest to the spirit of the era if you don't have a full roster of minor league players you can pick and choose from. You will have some players you can't use now but want to keep, and they are the relative handful of players who appear on the minor league rosters, having been farmed to your particular friend in Baltimore or Milwaukee or San Francisco -- although probably in reality nobody ever dealt with only one team at any minor level. Since the minor operator is still independent, though friendly, the Joe Unknowns who make up the invisible portion of those rosters are the players who are not yours, but remain the property of the minor team.
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