Itinerary Help please - 9 days in Oct/Nov

If you love big cities so much why not spend all your time in Tokyo? You can visit Kamakura as a day trip to see a couple of temples and you can visit Hakone for the onsen experience.

Visiting Osaka doesn't add much when you have already seen Tokyo. You have only 9 days.

I've heard good things about Kyoto and Hiroshima

But do you want to visit these places? It is up to you.

Are those 9 full days of sightseeing, or more like 7 days after you subtract arrival/departure days?

I've heard good things about Kyoto and Hiroshima but am concerned about commuting, from what I can see the JR pass doesn't look that economical getting between those 3 cities.

These are not really commuting distance. Could think of visiting Hiroshima/Miyajima as day trip from Kyoto, but it would be a long and tiring day. Kyoto itself is worth at least 3 days.

Not sure, why you think that the JR pass is not economical for these 3 cities. These are very long distance trips and if you go to all three cities and return to Tokyo within 7 days, a 7 day JR pass would save you quite some money.

I'm also keen for an Onsen experience.

Depends on how much time/money you want to spend on this. Onsen are all over Japan.. However in my experience, whatever calls itself "onsen" in the big cities is rather artificial ("sento" are authentic and worth a visit though). You don't need to travel far from Tokyo to be in nature/mountains/onsen, so could do this easily as day trip. Some of the best onsen are rather far though and with an overnight stay you would realistically need to budget two days for this, not sure you want to spend that much time of you short trip.

With 9 days (or 7 days), I'd either split time between Kyoto (Nara) and Tokyo or base myself in Tokyo and do some day trips from there to e.g. Kamakura, Hakone, Nikko (better as overnight). The first option would give you the best of traditional and modern Japan, but would be more tiring. The second would still allow you to see some good temples/nature, but should be more relaxed as you don't have to move around all that much.

I agree with bamse, either 3-4 days in Kyoto and 3-4 days in Toyko or base yourself in Tokyo with short trips to Hakone/Kamakura/Yokohama/Nikko.

On such a short trip, I would far prefer the latter, basing myself in Tokyo and doing a few short trips. More relaxing, easier, and about $200 cheaper.

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