The other reason is the "strength" of a farm system is primarily the players a couple years from the majors. Phillies have been thin there for years, and traded a number of players in that pool. Outside of a few outliers, most players in low A and below add nothing to a system's perceived strength b/c it's too early to evaluate them. Phillies have focused on the bottom of the system the last couple years, shaking up scouting, adding developmental resources. Last year Clearwater had a great season. If progress is being made we should see improvement at Jersey Shore and continued above average play at Clearwater, if prospects develop.
One thing to watch going forward, as teams keep players in the DR longer due to roster limits, the quality of play in the DR should probably approach low A level, and the better DR players may start skipping the FCL and go straight to Clearwater.