The originally cited article is riddled with inaccuracy and omission. Just a few from page 1: the ASG was not involved in the plot to kill the Pope in Manila, they did not provide sanctuary to Ramzi Youssef, and the American missionary couple kidnapped by the Abu Sayyaf were collateral damage in a move aimed at a specific non-American target, not a target in themselves. This is so typical of reportage on the Abu Sayyaf, especially from the big-name parachute journalists who occasionally deign to grace us with their presence, that it no longer raises an eyebrow. When I got to this bit, though:

It struck me that the most pressing problem in today's Philippines isn't terrorism or even government corruption but poverty and a lack of social mobility.
I have to admit that I had a rather severe encounter with the "thank you for that astonishingly perceptive observation, now excuse me while I gag" moment. What is it that possesses Americans and persuades them that they can walk into environments of which they are clearly ignorant, look around in a full circle, and gravely pronounce to the world what "the most pressing problem" is... through the good offices of The Smithsonian, who really ought to know better? The superficiality is almost blinding.

Looking at the pieces cited on this thread, I have to say I don't for a minute believe that our people on the ground here are as ignorant and naive as they come across, and I suspect that this theater is simple being used, as so often before, as a source for a few feelgood stories.

There has been no terrorist attacks on the U.S. from a number of countries where we both have troops and don't have troops. The metric in itself is completely irrelevant.
If this is the metric of choice we'd have to wonder why we're in the Philippines in the first place. Some people who have attacked the US have gone to ground here, and the explosives acquisition for the Bali bombing was done here, but have any of the groups here directly attacked the US?

Ultimately the solution in the S. Philippines is a political solution, but JSOTF-P was immensely successful in reducing the level of violence in the region. It is time (has been time) for the diplomats to take advantage of the reduced violence and implement a sustainable political agreement.
A sustainable political agreement is extremely unlikely, and there's very little that diplomats can do to produce one, let alone implement one. We tried once before, with support and pressure for the MOA/AD with the MILF, and managed to make matters worse. Possibly unwise to repeat.

So if the mission to defeat terrorist networks and to eradicate safe havens has been successful, why are U.S. Special Forces still operating in the southern Philippines?
I suspect that we've accomplished all we're likely to accomplish, and it wouldn't surprise me at all to hear that we're maneuvering toward extrication. Of course that would mean a return to business as usual (and the word "business" is not there by accident) but that was always going to be the case.

This is fantastic. When I was part of OEF-P in 2002 we weren't allowed to even think about staging operations on Jolo.
In 1982 I spent a fair bit of time on Jolo and Basilan, among other places we don't go now... alone. Things were different then; couldn't have done that in '72, '92, or '02. Still, it was... interesting, for want of a better word. Also interesting, the editors with whom I discussed plans to write about the situation all told me that the Muslim conflict was over and done, and the issue was Marcos vs the NPA. Tides ebb and flow; it is their nature. Fundamental change... maybe someday, but I suspect not in my lifetime.