I'd go with something on the fall side of the spectrum instead of a bulky, overly warm winter coat.
Something like this is what I wear when I visit Japan in the spring/fall:
http://www.patagonia.com/us/product/...390-1&pcc=1128. Warm enough for most conditions, easy to add a sweater underneath it, and small/light enough to stash in your backpack if you get a warm enough day.
I wore this kind of jacket when I was there two weeks ago and the weather was just a little warm for it then, so it should be a decent match for the timing of your visit. Have a great trip!