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While I understand what you're say, Doc ... the truth about specs - ALL SPECS - is that they do not get better simply by aging, (though this is what the age-arc charts would have us believe).  They get better by LEARNING something.  So, yes - it is completely fair to judge a player based on the past performance of the farm system - because that farm system is the one teaching him.
While some 'savants' will perform the same regardless of environment -- by and large, if your student has a choice between an impoverished inner-city school vs. Beverly Hills 90210, that student is WAY likely to have a completely different performance arc depending on which school he ends up at. 
Of course, if you're constantly drafting players with 800 SATs, you're going to get different results than if you're drafting those with 1400s.  Where you draft matters.  You don't get a shot at Griffey or AROD or Strausberg if you're winning 95 a year.
The reason I used the Braves as my comparison, (other than I'm most familiar with them), is that they were drafting in the 20s for much of the past 20 years.  They were not advantaged by winning 60 each year, (like a KC or Pittsburgh or Milwaukee).  The Ms were a generally winning franchise until Bavasi -- but even at that, they've had winning records 2 of the past 3 seasons. 
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Additionally, I didn't mention pitchers, specifically because the Ms do have a much better track record with pitchers in this time period, (especially relievers).  I've noted that as a strength in the past.  But, the list that started this thread was severely (and oddly) heavy with position players.  Personally, I'd be thinking if anyone got shortchanged, it was guys like Kasperek. 
I "hope" that Z has changed the direction of the farm - primarily by skewing away from the quick-twitch types and looking more at baseball smarts.  But, that isn't exactly a good sign for the quick-twitch types already in the pipe.  If they were "800 SAT" players *AND* the new regime doesn't believe they'll adapt -- that shouldn't change their projections upward.  And, as you note - it'll be 3-5 years before Z's prospects start getting enough MLB time to begin making an informed decision on them.