Leather soles are not practical in Japan or for travel most of the time since you will be walking a lot and they may get wet. I like leather soles normally but never travel with them. If you expect lots of tatami restaurants, avoid laced shoes.

I normally just travel with the shoes I am wearing and had gone into Haleakala crater and to meetings on the same trip. Try something comfy like Rockports or similar.

I pack leather soles only when there will be a formal event.

Agreed. In Japan, loafers are your friend. They have the added bonus of looking good and being conducive to air travel (easy to remove at security and while in flight).

I've been wearing uber-comfortable Kenneth Coles around here, but will probably switch to something more robust very soon. Life in Japan, where sitting is often a luxury, takes a lot out of your shoes.

Given the time of year, I plan to wear jeans mostly but was debating a pair of khaki's as an alternative and so I could be a little dressier if need be. The shoes I am debating are plain leather tops with rubber soles. Think of a dressier Doc Martin.

I would prefer slip-on shoes but it's not a possibility at this time (funny shaped feet and no time to break in). The primary shoes I will be wearing are a low cut hiking/tennis shoe hybrid, dark brown/dark blue uppers with an aggressive tread. They have a quick lace hook system at the top and are goretex lined. They can go pretty much anywhere but wouldn't look right with tan khakis.

If you're in Tokyo on the second Saturday of the month, then there's this 'people watching' opportunity:

http://en.wikipedia.org/wiki/Kimono_de_Ginza

Photos of past events here: http://gojyaku.hp.infoseek.co.jp/ginza-index.html

They've even published a guide on how to deal with tourists
http://www.kimono-office.com/eigo/eigo_set.html

(Next one is the 8th March. Sorry! Don't think you'll be around. Oh well, I'll still post this in case anyone else is interested)

Don't have time to read the whole thread, but has anyone mentioned that you don't have to validate your JR Pass the moment you arrive?

I've arrived in Japan, spent a week or two in Tokyo or Kyoto, and then validated my JR Pass (doable at any major train station) for journeys around the country. Your pass is valid for 7, 14, or 21 days from whenever you validate it, not from your arrival in Japan.

If your hotel is toward the northern end of the Yamanote line, i.e. within a couple of stations of Ueno, you can save money by taking the Keisei Skyliner into Tokyo's Keisei Ueno station. I think it's something like ¥1750 these days.

If you're staying at a hotel that has direct bus service and you're not arriving at rush hour, that can't be beat for convenience.

For convenience (although not money saving) in traveling within Tokyo, get either a Suica or a Pasmo card. These are debit cards that work on all trains (JR and private) and subways in the greater Tokyo and Yokohama area. They allow you to take advantage of whichever mode of transportation is easiest for your particular destination. They're available in increments of ¥1000 and can be replenished at any train or subway station.

Just to be clear -- The list of stations which have offices that can exchange a JR pass voucher for a JR pass is here:
http://www.japanrailpass.net/eng/en009.html

The pass does not necessarily have to start on the date you validate it. When you visit the JR pass exchange office, you can specify the date on which you wish to start using it. That date can be days or even weeks later.

Regarding footwear, there is this thread:

Travel Shoes for the Urban Japan Jungle