This question makes an assumption that's not true. Already in 1905 Japan was able to win a war against a western power (to be fair, a weak one), and Japan was highly modernized by the time World War 2 began. It wasn't some backwater country lacking in industrial development by any standards, as your question seems to imply.

Japan--very importantly--was also never a colony, and the Middle East as it exists today is a direct consequence of post-Ottoman colonial dealings by the British and the French. Policies aimed at resource extraction for the benefit of colonial powers don't seem conducive to local development.

John Dower, a historian of Japan and author of "Embracing Defeat: Japan in the Wake of World War 2," wrote and spoke on this topic multiple times. Here is a link to a short article written in the early months of the Iraq War. In it, he looks at both factors within Japanese society as well as actions taken by the Americans, both which contributed to the success of the Occupation.

For example, from the Japanese perspective, Japan already had a history of democracy. To be sure, it fell well short of full enfranchisement and did not last long before the military took full control, but it provided some precedent. And concepts like women's rights were not new (in fact, Margaret Sanger had visited the country several decades before). These contributed to the successful adoption of democracy and enshrinement of gender equality in the constitution. Japanese society, though exhibiting a wide spectrum of beliefs (from conservatives to communists), was still largely cohesive--unlike the strong religious and sectarian divisions present in Iraq. And Japanese structures of government basically remained the same, though with the notable absence of the military.

The Americans, in turn, implemented reforms that were truly popular--particularly land reforms motivated by the American New Deal, which greatly benefited rural farmers. In the urban setting, strong labor protections were implemented--and here again, Japan had a history dating back to the early Meiji period of labor protections to provide precedent. There were little-to-no "spoils of war" for the Americans. No domestic resource like oil, no profiteering contracts to American corporations. In contrast to the emphasis on privatization in Iraq, the American Occupation emphasized, in Dower's words, "pro-state and anti-foreigner" economic recovery.

The Americans also refrained from bringing in large cadres of untested foreigners to design and oversee the Japanese economy. Dower notes that this task largely fell to the Japanese themselves, and while it was at first a difficult one, it meant all the effort previously directed to military production was now unleashed on civilian enterprises. American involvement here was not in the form of direct-investment, but instead in the form of access to licenses and patents, as well as concepts like quality control procedures.

Obviously there are many more reasons, but hopefully that addresses some of them. I really recommend Dower on this, he has several articles freely available as well as one or two video lectures directly comparing Japan to Iraq.