One of the great dangers of doctrines and models is that once we adopt them we become enamored of them, and when reality doesn't fit the doctrine or model, we try to modify reality instead of changing our perceptions.
In the southern Philippines the core conflict, the conflict that kicked off the violence in the early 70s and sustains it today, is not between "the government" and "the populace". It's between two portions of the populace, both of which consider themselves aggrieved. One of the great failures of governance in this conflict was the decision of government to take the side of one portion of the populace against the other. One of the major causes of the failure of the recent US-supported "peace agreement" was that it treated the problem as a dispute between government and insurgents, and excluded one of the contesting populaces from the process. The task of government is not to reach a peace agreement with the insurgents, but to broker a peace agreement between two portions of its own populace that have irreconcilably different demands, neither of which trusts the government or each other. Not easy even for a functional government with some popular support for a peace process. For a largely dysfunctional government with a populace clamoring for a hard-line approach... beyond not easy.
There we agree.
The perception of "kept beyond their control due to the actions of some manipulative foreign power" doesn't really exist here. The bulk of the Muslim populace here has a reasonably positive perception of US involvement, which they see as a controlling factor on the Philippine government. There's probably more distrust of US motives on the settler side. One of the odd quirks of all this is a widespread belief among Mindanao settlers that the US has cut a devious deal with the MILF to support a breakaway in return for access to "the oil" and base rights. There's no hard evidence that there is any oil or that the US wants a base in Mindanao, but that never stopped anyone from believing!
Thailand has an intractable problem with Muslims in the south, Indonesia has all kinds of simmering ethnic issues and separatist sentiments, Vietnam and Laos have issues with their ethnic minorities... it's still being worked through all over SE Asia.
I'd be very, very hesitant about trying to assert a US role in that effort. It's possible that we could help; it's also possible - and I think rather more probable - that we can make things worse. We don't understand these issues as well as we think we do, and we often seem reluctant to listen to those who do understand them. Subtlety is needed, and that's not traditionally a US strong point.
Yes... not to mention a civil war of positively African proportions, one of history's great genocides, and various other digressions. Europe was even worse: it took them centuries of almost continuous war to arrive (assisted by exhaustion) at the current level of peace and stability. In much of the world that process was frozen by the colonial imposition of order at the expense of stability. Now it's thawed out. No real reason why we should expect it to be any prettier for them than it was for us.
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