Briefly, Moro separatism is nothing like the force it was at its peak in the early 1970s, when the old MNLF had 30,000 under arms, out of a population of about 2-3 million Moros. Marcos was a master of realpolitik and he sapped the MNLF of its main raison d'etre, when islamic practices were recognised in Filipino law and autonomous status was granted to four majority Muslim provinces. This caused the MNLF to splinter and many fighters left the war altogether.
That said, (much like Aceh) the handling of the remaining militants has been poor, hampered by the usual problems of professional armies fighting guerillas on the guerillas' own turf, the aforementioned corruption and (allegedly) the MILF's assistance by newer Islamist groups from other parts of South East Asia & the Middle East. I have my doubts as to whether the latter amounts to very much in reality.