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The differences between the US occupation of Japan and Iraq are suggestive. The US fought Japan in exhausting war and had every reason to hate its government. Democratic America detested Japanese monarchy. The Western Christians were xenophobic about very strange customs of the Japanese. Yet the US was wise to change none of that.
America strengthened the very Japanese institutions that underpinned the war, and only eliminated Japanese army, the direct threat. Then the US used those institutions to change the Japanese outlook from within. The mid-term result was hugely successful: Japanese ambitions were channeled in the economy, and the economy directed outward. The long-term change in mentality is unlikely, and Japanese imperialism would re-surface, reinforced by economic successes. Hardly any policy, however, could provide more than mid-term results.
Contrast the American policy in Iraq. The US destroyed the institutions such as the strong government and police which cemented the multi-ethnic religiously diverse Iraq. Reforming a failed state is impossible; only strong states survive the reforms. America made the situation still worse by directly enforcing the law and pushing for the unwelcome political changes like democracy and Westernization. No people would accept new ideology force-fed to them by hostile outsider. They will fight or, at best, remain contemptuously passive. Once the occupation force withdraws, locals will run for the golden old values in their most extreme form. Population will firmly connect the resistance fighters with idealized old values, and elect them to power.
America could follow the Japan example in nuclear Egypt, Iran, and North Korea. All of them still have strong security apparatus and reasonably conformant population. America may concur their capitals, install acceptable rulers without damaging the security framework of the countries, and have the new rulers brainwash their citizens with local variety of the Western ideology, from schools to mass media. Ataturk was almost alone when he started secularizing Turkey. Totalitarian governments plus the Western ideology could solve the problem of nuclear rogue states.