In my opinion, Japanese koi are far more superior.
I have seen stunning small koi from Taiwan, only to develop badly. It also happens with Japanese koi, but because of their top quality breeding stock and breeding programs, the end product is normally much better.
Another huge difference is that culling by the Japanese is being done by experts who have done it for decades, and they will cull much more than the Taiwanese. They take more pride in their fish. That is why you often get good and bad koi in a Taiwanese batch, but in a Japanese batch, mainly good quality and top quality. I would say the emphasis in Taiwan is quantity and in Japan on quality.
I have heard and seen from their websites that most Taiwanese breeders use Japanese koi as their breeding stock. It means that they themselves, have more faith in Japanese koi.
I also believe that Japan has a more stringent approach towards KHV.