I think the risk here lies in clinging to the idea that we're still dealing with coherent organizations with set goals and interests. I don't really think that's the case. Certainly there are individuals and small clusters with the incentive and capacity to make a mess, and that needs to be dealt with, but it requires a different emphasis than what an organizational focus would suggest.

ASG is a bit of an anomaly. The group has been most visible and drawn the most aggressive response when its political concerns and affiliation with international jihad have been at their lowest points: when the group was a high-profile bandit gang with a very nominal Islamist agenda. From a terror perspective, the group has been most dangerous when its criminal activities have been suppressed and the small Islamist core tries to track the remaining organization back to its jihadi roots. That happened in 2003/4, when Khadafy Janjalani was forced to run out to Cotabato. He ended up linking up with the Manila-based Rajah Solaiman Movement, composed largely of Filipinos who had converted to Islam while working in the Middle East, and the outcome was the 2004 Superferry bombing. That link looked to be a real problem for a while, but RSM was taken down, breaking the Manila link, and Janjalani was eventually killed as well. While there's currently no leader of KJ's visibility, it's certainly possible that someone with similar views might try a similar maneuver. It's entirely likely that a small cell composed of JI veterans and former ideological core members of the ASG might try for a high profile attack to put themselves back on the map and draw some resources, and a small cell would be in many ways more dangerous than a large organization.

I'm not at all sure that "we", as in the US, can "win", because it was never really our fight to begin with. All of the conditions to support insurgency still exist in the Tausug/Sama region. What will result from those conditions remains highly uncertain. It would be superficially logical for the MILF to expand its influence into what is now a leadership vacuum, but the Maguindanao/Maranao dominance in the MILF has always been an obstacle to that. An MNLF resurgence seems equally unlikely. Some jihadi groups might try to pick up the slack, but they will have to focus on the local concerns and the local agenda to gain much traction: the populace really isn't much concerned with the global jihadi agenda.

We'll see. Very hard at this point to say what will emerge, but it's not likely to be peace. Trying to analyze or understand the situation in an artificially imposed GWOT context is not going to produce any useful conclusion.