The reality is of course, is that "it's complicated."

On this we agree.

We must get straight with the central government before we can get straight with the problem in the south. (Same, by the way is true in Afghanistan, Pakistan and many other places).

The problem is that "getting straight" with each other is not a thing that governments and politicians are particularly keen to do. I'm not one, so I don't pretend to understand their rationale. Far easier to focus on some secondary or tertiary manifestation of poor governance, and send the military in to "resolve" the problem there instead.

I suspect that the problem is not entirely a need for the US and Philippine Governments to get straight with each other. What is needed is for the Philippine Government, and the Philippine governing class, to get straight with their own people, and to confront the reality that the traditional prerogatives and privileges of the Philippine governing class (primarily effective exemption from the law) are fundamentally incompatible with effective governance. US objectives in the Philippines will not be achieved until this happens, and there is very little the US can do to make it happen. This has caused a lot of frustration and will cause a lot more.

Military victory - or at least a level of dominance that could pass for victory - has been achieved in Mindanao on a number of occasions. Without effective governance, the conflict simply re-emerges, often in more radical form. Effective governance cannot be achieved while those who govern are above the law and are free to use that privilege to advance their personal interests.

Realistically, even with effective governance the Mindanao conflict would be very difficult to resolve. Without it.... close to impossible.