Germany and Japan were drastically different. They had a homogenous population, and their government structure could be used almost as it was with a new political system. In Germany, for example, many ex-nazis kept their position in society.
Iraq on the other hand is a state whose lines were drawn by a colonial rule and contains diffenrent populations. Saddam ruled using a minority ethnic group as the ruling class, which created an internal ethnic tension that was not possible to solve with an outside intervention.
In western Germany the denazification stopped very early despite our legends about 'nazi hunters' (the Mossad being the only agency that kept doing the real work), but it lasted two decades in east Germany, and no ex-Nazi kept their positions.
Iraq on the other hand is a state whose lines were drawn by a colonial rule and contains diffenrent populations. Saddam ruled using a minority ethnic group as the ruling class, which created an internal ethnic tension that was not possible to solve with an outside intervention.