The deficiencies raised by the FAA can be administratively fixed without the need of a new organization i.e. Philippine Civil Aviation Authority (PCAA).
If you have read the House Bill 3156, it transforms the ATO into an independent agency...Philippine Civil Aviation Authority. The bill exempts the new regulatory agency from taxes, customs and tariff duties in acquiring supplies and services used for its operations. Upgrading the ATO will only set up another vehicle for corruption.