Okay, I must concede that major league coaching may be part of the issue. Marlon Byrd has all of a 1.1 WAR for the Phillies. He put up a +3.4 WAR in his first full season in Philly, then -2.1 the next season in Philly, then gone just a little into the next season. Traded straight-up for the immortal Endy Chavez, who put up a -0.4 WAR in that one partial Philly season and allowed to leave as FA.
Michael Bourn was excoriated by Phillies minor league staff for taking walks instead of collecting HRs and RBIs. He had +0.7 WAR for Phillies. He did bear fruit as key part of Brad Lidge trade, without which we don't sniff the 2008 WS
Jason Michaels did put up +5 of his career +5.6 WAR in Philly, making him the leading direct WAR contributor to Phillies, apart from Burrell. Bourn with the greatest overall impact.