In my time covering the Pittsburgh Pirates farm system while Neal Huntington was the General Manager, I noticed a transition in the organization.
Prior to Huntington, the Pirates didn't have great communication in their minor league organization. One of the biggest things that Huntington and farm director Kyle Stark did was turn the Pirates' player development system into a more cohesive unit, rather than the disembodied mess it was under Dave Littlefield and every General Manager prior.
Thus far, under General Manager Ben Cherington's "build" strategy, I've seen this cohesive minor league system maintained, with a few upgrades.