My attempt a Japan.
I first moved Japan 1E as a whole. But I doubt if that is something that I think should be included.
I started with Hokkaido. I think the old shape looks odd, even when looked at it from an angle. I like the shape that TJDowling used in
this post, although I think it is a bit to large. I removed 2 land tiles from it. (Yellow and red circle) I place an islands feature in the red circle. This is meant to both represent the northeastern part of Hokkaido (which I removed) and the Kuril Islands. An extra islands features could be added 1NE for a better (aesthetical) representation of the Kuril Islands.
Then I tried to focus on the area around Tokyo. I tried to enlarge it, but all of my attempts looked horrible. I like the current shape of Kyushu and Shikoku actually. The only downside is that they are connected, instead of having straits. In the end I didn't make any change in the shape of Honshu, Kyushu and Shikoku. But I think that that area already looks quite good.
I redistributed some resources of Northern Honshu. I moved the pig to Hokkaido (to represent the agriculture significance of that island. It is 1/4 of Japan's arable land, but first in rank of agricultural production)
I moved 1 of the silk resources inside Tokyo's BFC and the other to Shikoku. (I don't know if that is historical, but it fulfills making northern Honshu less attractive quite well IMO)
I also added an island feature 2S of the Tokyo tile, to represent the Izu islands. This also makes Kanto a bit stronger.
As mentioned, I place one of the moved to Shikoku. I also move the gold of Kyushu 1N. This allows Kagoshima without it being placed on a resource. (Nagasaki could also be an alternative city on Kyushu, but I think that Kagoshima is historically more important.)