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Ghost,
What I see is that wOBA for pure rookies is predicted (by marcel) to be .335 and comes in at .319. This is indeed a bit greater than the error in estimated production of other classes of players (all MLB'ers), but I would suggest that it is still pretty reliable. As well, the hiccup may be in the model and the way MILB numbers are crunched, not in the reliability of the crunching.
But I may have missed something here.
moe