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The makeup of pitchers is arguably the most intricate and hard-to-understand aspect of the game engine. So many different factors go into the final profile, so many elements play a part in how they perform.
I basically create most of the NeL players using their basic import as a shell only and stats according to my own methodology, and it is super tricky to get them right. Era (as in chronology, not Earned Run Average) plays a huge role in their final makeup, with pitchers from the earlier years profiling almost invariably as finesse pitchers with lower stuff and individual pitch ratings and higher movement and control, and the opposite becoming more prevalent as time progresses. At first I sought to try and correct this, but then realised you have to work with the AI not against it and just accept that this is how things are. The pitchers still seem to come out with appropriate levels of performance, which in the end is what counts.
With regard to your specific enquiry, you'll most likely find that you're seeing what you're seeing because of the first point Pelican raised, namely their point of reference. Sounds to me like these MiLB pitchers' ratings are being referenced against the level they are currently at and will drop as they move up.
You can usually see a player's true / raw ratings by toggling off the All player ratings are displayed relative to box in global settings.By leaving this ON but choosing the various levels in your save, you can also go into the player profile and you'll see how it changes their ratings with each level selected.
Not exactly a solution, but I have found the more I am familiar with the inner workings of the game engine, the better I understand how these end results are settled upon.
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