While you wait for a new answer, you can check this old one from /u/ParkSungJun
This is not an answer on how Japan treated Taiwan in comparison to its other colonial possessions. I am just pointing out that the premise of the question is incorrect. Most of Japan's ex-colonial possessions have positive view of the country. Per research conducted by Pew Research in 2015 while not all of Japan's colonial possessions are in the results, of the ones that are only South Korea and China have a negative view of Japan. I believe this is strong evidence that what happened after WWII has a much stronger impact on a country's current image than what happened before and during WWII.
So I've heard from many Taiwanese people that despite being a Japanese colony, the standard of living went up a lot under Japanese rule, so I went ahead and investigated.
If you look at Agricultural output up until Japan started getting bogged down in WWII (so up until 1940s), every category was going up. One study show that from 1910 to 1937, the total output of agriculture went up 180%, with an annual rate of growth anywhere from 1.21% to 2.98%. And this is in basically every category of agriculture (the study classified it into main crops, special crops, auxiliary crops, and fiber crops). This can be compared to Japan's 1880 to 1920 Agricultural total growth of 180%.
The next study I looked at was about trade. The growth of trade was high in Taiwan under Japanese rule. Exports grew higher than imports too. Through semi-complicated math modulated by price indices, exports grew by 16.9% while imports grew by 14.9% (this is looking at 1896-1935). You can compare this to another Japanese colony of Korea where exports grew by 8.7% and imports grew by 8.2%
The next important metric I looked at were wages adjusted for inflation (real wages). The 1915-1933 real wages increased in all the major sectors, and some of the average annual wage increase percentages were higher than that of even Japan. For example, the average annual percentage real wage increase for manufacturing in Taiwan was 5.6% for males and 5% for females, compared to 5.1% for males in Japan and 2.8% for females (Korea only saw a 1.9% annual wage increase for males in the manufacturing sector).
Finally, to understand the context of what it was like before Japan took over Taiwan as a colony, I found a very great peer-reviewed article written in 1942 describing Taiwan under Manchu rule:
Political conditions on the island had not been favorable to economic expansion. The administration was in the hands of Peking officials who paid little attention to the local interests and who conducted affairs in mandarin which was unintelligible to the local population speaking Fukienese and Cantonese dialects. Land relations were feudal, and marked by frequent agrarian and clan riots. There had recently been some attempts to reform and develop the island along modern lines, but these attempts were either abortive or nipped in the bud by the war with Japan. Yet certain improvement did take place. The area under cultivation was increased, the harbors improved, the railway and telegraph introduced.
That's all I got for you. I could probably look at more figures (but I'm honestly already going too much into economics), so if needed maybe I'll look more tomorrow since it's super late here. Also, there seems to be a really good answer here too (maybe more in standard historian type answer).
I'll stick to comparing Korea vs Taiwan's relationship to Japan since that's what most of the academic literature is focused upon.
To showcase how fondly Taiwan remembers Japanese rule, let's look at how Lee Teng-Hui, Taiwan's first democratically elected president, went so far as to visit the controversial Japanese Yasukuni Shrine, which enshrines Class A war criminals from WW2.
And, even though there were Taiwanese comfort women victims too, he said "China spreads lies such as Nanjing massacre to the world ... Korea and China use invented history as their activity of propaganda for their country. Comfort women is the most remarkable example."
If you ask an Taiwanese person why Taiwan fondly remembers Japanese rule, their response will be something like how Japanese rule was benign, especially compared to the KMT, and that Japan developed and modernized Taiwan.
But, Korea was a much more important colony for Japan than Taiwan. So, Japan poured more money and resources into developing Korea as well as sent its most promising future leaders to Korea instead of Taiwan. Japan deserves as much credit for helping to develop Korea as it does for Taiwan, although Korea had already started to develop a modern economy before Japanese rule.
And, Japan responded with brutal force on both Taiwan and Korea whenever they challenged Japan's authority. ParkSungJun mentions the Wushe Incident in Taiwan, but there was also the Beipu Uprising, Musha Incident, and the Tapani Incident. As many as 14,000 Taiwanese were killed in the first six months of occupation, and around 12,000 were killed from 1898 to 1902.
So if Japan was brutal to both countries and both countries were modernized under Japanese rule, why does Taiwan look back so fondly on Japanese rule compared to Korea?
One reason is that the Taiwanese national identity is a very new phenomenon. When we talk about Taiwanese identity today, we talk about how its a mixture of Chinese and Japanese influences.
So, when Taiwan became a colony of Japan, there was no such Taiwanese identity. And, without this Taiwanese identity, there was less resistance to Japanese rule compared to Korea. Korea had been unified into a single, independent state for around 1,000 years and had a proud identity that resisted being colonized.
Also, to resist, you needed leaders to help rally the resistance. But, when Taiwan was ceded to Japan under the Treaty of Shimonoeski, Japan gave Chinese residents the option to leave Taiwan to go to China or remain and become Japanese subjects. So, the people who left were the local Chinese elites who would have been the most opposed to Japanese control, had the most to lose under Japanese rule, and were thus most likely to rebel.
When those Chinese local elites left, it was this opportunity for a new group of local elites to emerge insofar as they collaborated with Japanese rule and therefore these new leaders were not going to rebel.
In contrast, the Korean local elite, the yangban, stayed in Korea and their standing and power was threatened by Japanese rule. Only a very small number of the yangban collaborated with Japanese rule, and the rest were more than ready to rebel against Japanese rule.
In both Korea and Taiwan, there's initial armed resistance that Japan brutally crushes with force. But, the Taiwanese later learn to accept Japanese rule because of the lack of a national identity and lack of leaders to lead this resistance while Korea continues to buckle against Japanese rule. The Wushe Incident stands out not because it was somehow harsher than other incidents, but because it happened so late after initial resistance had died down. (Okay, the picture of all those chopped heads is harsh).
And, this forms a feedback loop where the more the Koreans rebel, the harsher the Japanese treats Korea which makes Korea rebel even more and so on. And, the more Taiwan acquiesces to Japanese rule, then Japanese rewards that behavior and so on. Basically, the goal for both was the same but Taiwan was rewarded while Korea was punished to do what Japan wanted.
In Taiwan, the people opposed to Japanese rule had already left or had been killed off. And, those who would have remembered Japan's harsh rule died off with age. So, it left a younger generation like Lee Teng-Hui to grow up when Japanese rule had grown less harsh.
And, when the Kuomintang, KMT, takes over Taiwan after WW2, the Kuomintang displaces the local elites who had collaborated with the Japanese and now its the Kuomintang who becomes the new local elites.
Initially, much of Taiwan was happy about the Chinese controlling Taiwan. But, it was a rough transition. There was a million refugees fleeing from China to Taiwan, and Taiwan did not have the infrastructure to handle that influx. There was problems of hyper inflation, not enough housing, unemployment, and outbreaks of disease.
So the former elites, who were displeased about losing their power, used 2-28 to rebel and regain control of Taiwan for a few weeks. But, the Kuomintang responds with brutal force to regain control in a manner that you wouldn't have expected any less from the Japanese. It is estimated that 10,000 to 25,000 Taiwanese were killed.
And, this anger about the KMT soon displaces and replaces anger about Japanese rule until many Taiwan start to remember fondly the Japanese colonial rule.
There's this selective amnesia where those Taiwanese only remember the good things about Japanese rule and none of the bad things while simultaneously only remembering the bad things about KMT rule and none of the good things about KMT rule.
To quote from one of my sources:
When people talk about Japanese colonialism in the past, they often used it to compare to KMT rule... Basically, the history of Japanese colonialism is used for political reasons: it's a counterpoint for the KMT. Japanese colonial history is used to highlight KMT wrongs.
Sources:
Hechter, Matesan, and Hale: (2009). Resistance in alien rule in Taiwan and Korea, Nations and Nationalism 15 (1), 36-59.
McNamara, D.L. (1986). Comparative Colonial Response: Korea and Taiwan. Korean Studies, 10 (1), 54-68.
Suzuki, Shogo. (2011). The Competition to Attain Justice for Past Wrongs: The "Comfort Women" Issue in Taiwan. Pacific Affairs, Vol. 84, No 2. 223-224