Japan, China, and South Korea were never colonized nor significantly ruled by foreign powers and they're doing great.
- China: Qing Dynasty, 1644 - 1912; China was invaded by the Manchu army lead by Hong Taiji and Durgun. Manchu replaces Chinese as administrative language for first decades of rule, Manchu officials replace Han officials in highest administrative posts. Manchu dress and hairstyle are mandated on all subjects on pain of death.
- China: Yuan Dynasty, 1271 – 1368; China is re-instated as a country by Mongol ruler Kubli Kahn after his ancestors Ghengis and Bantu absorbed it completely into the Mongol empire. Chinese subjects are denoted as fourth (and lowest) tier subjects after Mongols, central Asians and Europeans. Chinese subjects are forbidden to use given names, instead being assigned a family name and a number.
- Korea: Japanese Empire, 1910–1945; Sovereignty of Korea transferred completely to the Emperor of Japan and exercised in person by the Governor General (a Japanese national). Hundreds of thousands of Korean women abducted and used in military brothels and possibly millions of Korean workers deported to work on infrastructure projects throughout the empire.
- Japan: Occupation Period, 1945–1952; Japan's unconditional surrender as per the Potsdam Declaration made Japan a military governorship under the Supreme Commander for the Allied Powers, General McArthur. Japan's current constitution was written, including it's current system of election, legislation and public service was devised under the absolute military rule of the United States. So much so that most Chinese still consider Japan to be a semi-independent satellite state occupied by the United States.
What about Vietnam, the Philippines, and Mongolia? Are their genes so different that they missed out on the Chinese/Japanese smarts?
Mongolia was never a colony. It was still lead by the Borjid Dynasty, who were treated by the Manchu Asin Gioro as a particularly honored Vassal. Many empresses dowagers of this period were Borjit princesses, including Xiaozhuang Empress who acted as regent for the young Kangxi. They also ruled over China for a century and made a giant mess of it, which is the key reason Chinese have historically often considered them to be somewhat mentally inferior (though they probably aren't, just their territory doesn't lend itself to intensive farming or city building).
Philippines and Vietnam are better compared to other South East Asian nations, rather than North East Asian nations. Thailand was never a colony, but it's not doing so great. Malaysia, Singapore, Brunei however all were and tower over all Asian nations but Japan in standard of living. Hong Kong was a colony too and if treated as a country is possibly on average the most prosperous on earth.
In fact, if you look Hong Kong, Malaysia, Singapore and Indonesia, all former colonies, you will find that the Chinese ethnic group does extremely well economically whether they go. Particularly when you see how well the Chinese do compared to the native Malays in economic pursuits, you will see that cultural values make a lot of difference
So hence the north-south theory, the same as Europe. Northern societies tend to be more industrious since they have to endure the scarcity of food and heat every winter. Japan, China and Korea are all freezing f---ing cold in December-March and the trees are bare and fruitless, a human society if they want to survive here must spend its time preparing clothing, and stores of grain for the winter so they lend themselves to tens of thousands of years of economic focus. Vietnamese, Thais, Malays, etc. are not stupid, they're just not economically minded. You cannot starve or freeze in these countries, coconuts litter the ground and fish teem in the rivers and the sun shines warm every day, a bit of shelter from the monsoon and you can live indefinitely.
Colonialism is a red herring. Everything is more interesting if you actually learn about Asian history rather than trying to mold it to prove a point.