I think the Tokyo minimap should stay, but the railways are too much. If you want to increase connectivity I think you should put some ports or airports to connect the islands instead... I see there was this orientation in the previous versions, I don't get why this map needs to be that much more complicated; and while train is widely used there it isn't an excuse to make a massive railway system with giant bridges across the sea etc IMO. It's not a Railway map, it's Japan, we should have a feeling of Zen and not "crap, I need an Aspirin" about it
I agree it would be more interesting though if the connections were a bit more linear, it might become too alike to Malta else (and I'd hate that ><). But having a couple of connecting devices to do it wouldn't overcrowd the map as it is now.
Splitting Hokkaido in two is a good idea, but these "East" and West" names are a bit bland. Unfortunately the two major cities Sapporo and Hakodate are in the west, but it'd probably fit better to have Sapporo for the West and Asahikawa for the East (although you'd need to change the border a little seeing
this map. That way the beer drinker is also reminded that two widespread japanese beers are brewed in Hokkaido! Perfect really

One last thing about Hokkaido, you obviously don't have the place to put it where it belongs but the way it is now feels like it will induce people to think Hokkaido is actually set like that. While it's not CC's purpose to procure education for the geographically challenged, I think it'd be more map-like to have some kind of way to indicate it's not its real position... Not sure if another frame could really work there
If I understand well Tokyo is its own bonus and not part of the Kanto region; the Tokyo on the main map should be blue then; if you don't want to disrupt the color theme you could use one of the Tokyo symbols instead though:
http://en.wikipedia.org/wiki/Insignias_of_Tokyohttp://en.wikipedia.org/wiki/Tokyo_TowerWhich brings me to another important point, in which I agree a lot with what RJbeals said: this map reminds me of Japan about as much as the current Portugal map screams "Here is the land where Fado was born"

It lacks flavour cruelly. I kinda like what you did with the region textures but apart from the two northern ones they are pretty much invisible and even a bit like an annoying blurred background in some spots. It doesn't feel enough, especially considering the fact you're going with this brown parchment general background. The huge waves might not fit, but surely several cultural elements could (another reason to get rid of the trains and have more space!). For instance the title could be bigger, have a rising red sun or a temple gate,
Fuji-san would be great somewhere, and most important have kanji characters. The font you use is a good choice but it would really add up to have kanji next to it in both main title and maybe Tokyo... Besides the background you use screams for some nice calligraphy putted on it
In any case, great work, I'm really glad someone is coming up with a quality Japan map after so many years of failed tries!