Short answer: Nationalism and geopolitical strategy.

Long answer: Nationalism is a cohesive group identity based on a broad conception of shared historical experience, language, culture, or creed. The development of the "nation" is usually traced to the invention of the printing press in the 16th century, which allowed for the formation of an identity outside the local and contributed to a sense of shared experience with those within that linguistic community. Ben Anderson, one of the foremost scholars on the subject, calls the nation an "imagined community" for that reason - whether or not you ever meet many other members of your nation, you feel intrinsically linked to them through a shared and mutually agreed-upon identity.

This concept was a relatively new phenomenon. Prior to around 1500, identity was intensely local, with very few exceptions. Order in Europe and most of the world was hierarchical, with dynastic rulers extracting resources from their subjects through either allocation of capital or blunt coercion, with the result being a patchwork of sometimes overlapping jurisdictions without any meaningful sense of political investment on part of anyone outside of the elite.

Nationalism, which reached its zenith beginning around the Napoleonic Wars and extending into the 20th century, changed all that. With a sense of shared identity and community came a sense that the "nation" was the legitimizing force for government. This is articulated not only in the writings of the Enlightenment, but in Woodrow Wilson's Fourteen Points at the close of World War I. In emphasizing the "self-determination of peoples" as the primary factor in determining the legitimacy of the nation-state, Wilson implicitly eliminated every other form of government from having the same legitimacy in the eyes of the Western world. This convention has largely become reality, which is why you see the rapid atrophy of global multi-ethnic empires in the 20th century. The awareness of the people as belonging to an exclusive nation indicates that only the sanction of that nation can legitimize government. The USA simply annexing Japan (while also being a logistical nightmare) would have been anathema to the viewpoint articulated by the American president just a few decades before.

Additionally, while subjugation of conquered peoples is difficult to justify to a domestic population in itself, there is also the practical matter of having the Soviet Union and China standing as monoliths right next to those conquered states. Rebuilding them as bulwarks against regional aggression was much more expedient in the long term than expensively attempting to occupy them, which is why the Marshall Plan rebuilt Germany with astonishing largesse and MacArthur's occupation of Japan was remarkably benign. Making these defeated and defanged states into compliant allies much better served American interests than openly attempting global domination.