You can train ATFP until you are blue in the face but if your command has their heads up their asses and doesn't know how to properly utilize that training then it is a complete waste of time. If the Philippine military promoted their officers based more off of merit and less of off whose family had the most influence then maybe things would change.
The Philippines also legitimizes extremists and separatists by giving them autonomous regions to govern and allows them to set up and enforce their own stoneage muzzy judicial system. The US can't be blamed for the extremism in the Philippines. The inept Philippine government did that all on their own.