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Organizational results are rarely easy to track back to an obvious source.  Outsiders know next to nothing, (or nothing), about scouts, lower level coaches, etc.  And the "name" people turn over regularly, (especially for poor clubs).  But, as a general tenet, decisions and competence flow downward.  The better your top people, the greater chance you'll choose competent people below you, etc., etc.
If you have an owner who is incompetent AND a meddler, you've got major problems.  Even if he's churning his GM and Manager routinely, much of the organization responds to HIS wants, because people are generally more concerned about keeping their job than doing it right, (and yes, I know how idiotic than sounds).
In most cases, I think it is a case of organizational philosophy leading to repeating the same mistake, because the powers that be are unable to accept data contrary to their beliefs.  THEORY:  "You must have big bats to win pennants".  RESPONSE: "You draft sluggers, acquire sluggers, and maybe even tailor your park to aid sluggers."  RESULT: "You lose, ranking last in ERA."  CONCLUSION:  "We need MORE sluggers."
That above is hyperbole, but likely too true in too many cases.  The belief that if a little is good a lot will be fantastic permeates the human condition.  Seattle under Bavasi seemed to become absolutely paranoid about hitter Ks.  The club drafted these low k free swingers, promoted them, went out and got them on the open market, and led the world in fewest hitter Ks.  They also were near last in run production. 
Today, there's a new GM and Manager.  So, a new "type" of player is being recruited.  But, how many guys throughout the org are believers in the old philosophy?  I don't know.  How many scouts who were INSTRUCTED to look for this type of hitter are now getting a different set of instructions?  Again, I don't know.  I don't think anyone outside the organization knows. 
Moneyball was instructive on many levels.  One was the often contentious relationship between the GM and the scouts.  The scouts and coaches do have beliefs of their own.  But, when directives come from above, each person must incorporate the new directives into their personal belief systems.  As with all things, some will perform better than others.  And Sports in general, and baseball specifically, have long been VERY inbred organizations.  When you get an entire organization buying into something that doesn't work, problems can last a long, long time.  The problem usually persists because of beginning assessments with thoughts like, "Well, we know the problem can't be X ..."  So, you have to attribute problems to something else, sending your crew into the rigging to mend the sails, while water continues to pour into the hold from the gaping hole in the side of the ship from the reef you have run aground on.