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The quick suggestions I would offer would be the following:
1) For most of baseball history, the most common league size and alignment was an 8 team league aligned into a single division. Setting up minor leagues, at least initially, along this structure is a good choice, historically speaking.
2) For most of baseball history, there have been three AAA level leagues (International League, Pacific Coast League, and the American Association, the latter of which was folded after the 1997 season). So aiming for about three leagues per classification level at the higher levels mimic history reasonably well.
Another item for consideration, related to the above, is that the minors originally started up as local or regional independent leagues which later on became integrated into the current major-minor relationship we see at present. As a result, starting the minors with more but smaller leagues fits in closer with how they really developed.
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