Overall there has obviously been a lot of organizational, top-down change, I just don't think there was much at the minor league level in Klentak's first two years. Jordan and his minor league managers have all remained in place (with the exception of Wathan moving to the majors and them adding another GCL team). Jordan was with the Orioles before the Phillies so it seems their comfort level with him was always high. And most of the hitting and pitching coaches are not new and/or are Phillies lifers, with one exception.
Wouldn't surprise me if bigger changes are ahead, now that the analytics department and the expanded major league coaching staff has a year under its belt.