In the OOTP world, minor league system rankings are based on the number of players you have in the top 100 prospects list. The specific rank of each player is used for a tiebreaker. For example, team 1 has two prospects rated 2 and 5 overall while team 2 has two prospects rated 3 and 6 overall. Team 1 will have a better overall minor league system ranking.
Another problem is that the top 100 prospects report is very random after the first season. There is even more randomness when playing fictional leagues.
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