We went to Japan 7 years ago and are eager to go again to see more of the country. Last trip we went to Tokyo, Kyoto, Takayama, and Kurashiki. We definitely want to see Tokyo again as we loved it but would like to see some of the more unique parts of Japan including some onsen experiences. We were thinking about the following stops:
Day 1: LA to Tokyo
2: arrive Tokyo and spend night
3: Tokyo to Tsumago (or some other onsen town in mountains) Where to stay??
4: Tsumago to Shirakawago for a few hours then on to Kanazawa that evening
5: Kanazawa
6: Kanazawa to Hiroshima
7: Hiroshima
8: Matsuyama -- go to Dogo Onsen
9: Fly from Hiroshima to Akita then onto Nyutu Onsen
10: Akita to Yamagata to stay at Shirabu Onsen
11: Yamagata to Tokyo
12: Tokyo
13: Tokyo
14: Tokyo
15: return to LA

Is this too much traveling? Any strong suggestions about better places to stop? We want to see more of the country this time rather than more temples per se. Favorite hotels, onsen etc?

Also will it be too hot in September? If so, when will it start to get cooler?

Thanks!!!!

Tsumago and Magome in the Kiso Valley are easy to access from Matsumoto...therefore, go to Matsumoto and the Kiso Valley only once...either at the beginning or end of your trip.

I personally think Shirakawago is worth more than a few hours...I'd stay the night, as the atmosphere changes completely after the day trippers and tour buses are gone.

Kanazawa is 5 hours from Hiroshima with the fastest trains and best connections. Not a short trip. If you left Kanazawa early, you'd have only one day in there. If you left Kanazawa later, you'd have only one day in Hiroshima. Each place could use two days I think. From Hiroshima, too, Miyajima is a nice island with no cars, some deer, a nice small mountain, good hiking, a picturesque temple with gates in the water....worth a day there too.

Tsumago is not an onsen town. One of my guidebooks says that if you are going to Takayama then you should skip Tsumago. You've been to Takayama so you can skip Tsumago.

Gero is an onsen town. It is on the Takayama line about 75 minutes north of Nagoya and 15 minutes south of Takayama. That location is convenient for your itinerary. It is on the route from Tokyo to Shirakawago. There is one or two buses a day that go from Gero to Shirakawago (via Takayama), otherwise you would take the train to Takayama and then the bus to S-go. There are several onsen hotels in Gero to choose from.

Your Hiroshima - Matsuyama - Hiroshima - Hiroshima airport plan is mixed up. The hydrofoil between Hiroshima and Matsuyama costs 4000 or 5000 yen each way, not covered by the JR Pass. And it takes time.

You should go from Kanazawa to Matsuyama to Hiroshima to Hiroshima airport. OR you could fly from Matsuyama airport. It is a bit of a chore to get to Hiroshima airport, but it might have a nonstop to Akita.

Dogo Onsen is great. You should also visit Matsuyama castle.

From Hiroshima, the onsen town of Beppu is not very far. You could fly from Oita.

I know for sure that there are nonstop flights from Hiroshima (HIJ) to Sapporo (CTS) and Noboribetsu Onsen is not too far from the airport.

Nyuto Onsen is very nice and may be worth the travel you are planning. I don't know about Shirabu but think it is a bit out of the way.

I don't like making a case for skipping Nyuto onsen, but just off the shinkansen line back to Tokyo from Beppu you could visit Arima Onsen near Kobe and Hakone and/or Atami Onsen not far from Tokyo.

Actually, getting from Hiroshima city to a ryokan at Nyuto Onsen would be a bit of a trip. Bus or train to HIJ, then flying to Akita, maybe nonstop or maybe connecting in Tokyo. Travel into Akita city to get the Tohoku shinkansen. Get off after three or four stops then catch a bus for a long ride up and up and up into the hills.

Gero is about 45 minutes, not 15, from Takayama.

Thanks for the feeback KimJapan and mrwunrfl. I am trying to figure out ways to see more unique parts of Japan that may have fewer tourists and/or more of a local feel. I would also prefer onsen in a quiet town, not a busier modern resort feel. I had heard Beppu was more busy resort feel than quiet mountain onsen town. I probably prefer the mountains versus a seaside resort. That is why I was focusing on Tohoku and Nyuto Onsen area. I also love the train rides in Japan and had heard the ride between Tokyo and Akita on the Akita Shinkasen would be interesting. Since I also don't want to go crazy traveling too often and lugging bags every day, here's a shot at another itinerary. Please tell me your thoughts.
Day 2: arrive Tokyo spend night
3: Tokyo to Sendai taking Akita Shinkansen. To see Matsushima
4: Sendai to Kukonodate to see Samurai town then spend night there or go on to Nyutu Onsen.
5: Nyutu Onsen
6: Nyutu Onsen - different onsen in area?
7: Go to Akita to fly to Hiroshima. See Hiroshima that afternoon and evening
8: See Miyajima, stay in Hiroshima
9: Hydrofoil to Matsuyama
10: Morning in Matsuyama then train to either Himeji or Arima Onsen near Kobe.
11:To Tokyo by Shinkansen
12: Tokyo
13: Tokyo
14: Tokyo
15: Return to LA

I am skipping Gero and Kanazawa in this itinerary thinking they may be less unique than Tohoku area? Would you agree? Is there a way to fit one of these back in or would you recommend another stop altogether?

That looks good, esp. because you are much nearer to Nyuto Onsen the day before you go there. It is an interesting ride on the Tohoku and Akita shinkansen. You could make Matsushima a stop enroute, maybe spend the night of day 3 in Yamagata-ken at the onsen and then stop at Matsushima and on to Kakunodate the next day. But, your new schedule is a good one: the travel that you do the first few days is not far or complicated.

There is a JR hotel at Kakunodate that is a good bargain.

Where are you staying in Hiroshima? There is a Granvia hotel on the shinkansen side of JR Hiroshima station. Better than that is the Rihga Royal. Even if you have a JR Pass it is worthwhile taking the bus from Hiroshima airport into the city the bus to the JR train is a tedious route. The Rhiga Royal is a short walk from the bus terminal. I'd take the bus even if staying at the Granvia.

The hydrofoil ride is scenic, esp. at sunset, perhaps on the evening of day 8. Otherwise if you get the hydrofoil early in the morning of day 9 you could see some sights in Matsuyama and then go for a soak.

Hotel Patio Dogo is a nice hotel that is across the street from the Dogo Onsen honkan. Matsuyama has a streetcar line that ends about a block before the onsen. When you arrive at the Matsuyama hydrofoil port look for the bus to Dogo. There is a bus that goes all the way from the port through the city to the streetcar station at the Dogo end of the line

I strongly recommend stopping at Himeji. I have not been to Arima Onsen yet but my impression is that, despite it's mountain location, it is a built up area. After all, it is convenient to Osaka and Kobe (and Kyoto and Okayama ...).

Thanks.
Here's an alternative to going to Tohoku. Which route do you think is more interesting?
Day 3: Tokyo to Gero (or possibly fly to Nagoya instead of Tokyo on way in and do Nagoya to Gero this day)
4: Gero to Shirakawago
5: Leave Shirakawago in morning to Kanazawa
6: Kanazawa
7: Kanazawa to Mt Koya
8: Mt Koya to Hiroshima
9: See Miyajima, stay in Hiroshima
10: Hydrofoil to Matsuyama
11: Morning in Matsuyama then train to Himeji
12:To Tokyo by Shinkansen
13: Tokyo
14: Tokyo
15: Return to LA

Also, what would weather be like in September? Should I really wait until October if I do not want the heat and humidity?

That's a good itinerary too. Yes, fly into Nagoya. You could probably need only a 7-day JR pass for this. There is a bus from Nagoya to Shirakawago, fyi. I would go from Kanazawa to Hiroshima. After Matsuyama, stop at Himeji and continue on to Kyoto or somewhere for the night if it is not practical to go all the way to Koya-san the same day. Or overnight in Himeji. Point is, I would visit koya on the way to tokyo.

Thanks. So do you think the Tohoku trip will be more interesting or the Gero-Shirakawago-Kanzawa route? I am torn between the two and am not sure what the differences would be.

Also, any thoughts on weather in September to do this trip? Should I really wait until October if I don't want it too hot and humid?

I don't know about the weather.

Gero is an onsen town and not a secluded mountain retreat. Chubu is more accessible than Tohoku (this is good/bad). Kakunodate is a nice visit for a couple of hours to visit the samurai houses and stroll the small town (and the JR lodging is another reason for stopping there). Shirakawago is a nice afternoon and overnight stay. Kanazawa has several gems but it also a fairly large city (this is good/bad). It's your decision, but I will suggest that Nyuto Onsen is a place that you have to decide that you really want to go to and you'll need to do some research.

Shirakawago is different. You can go there just having heard that it was an interesting place. As soon as you get there you will understand why. It's obvious and accessible. If it is not your thing then get on the next bus and in two hours you will be in Kanazawa or Takayama.

mrwnrfl has given you great information. I can comment on the weather. September tends to be hot and sunny...the humidity breaks sometime early in the month, but it's still hot. Into October the weather becomes cooler, especially later in the month, but you get into a bigger chance of rain, even a typhoon or two. Either month is good I think...or as good as it gets. There really is no perfect time to visit, as there is always changing weather here.

A comment on onsen towns. If they are known, they are built up. If they aren't known, they aren't built up and will not likely have amazing bath facilities or hotels...just the basics. Onsen towns tend to be built up in the concrete block style. Gardens are lovely, but architecture leaves a lot to be desired I think.

Arima Onsen is very built up in the typical block style, with a few nicely designed older places with style. Expensive.

Near Kanazawa, Yamanaka might be nice for you. There are more old style places than new, and there is some accessible nature. Most places guests do not leave the onsen hotel during their stay...in Yamanaka, there is a nice nature path and a cute town. Yamashiro nearby is similar but smaller. If your image of onsen town is traditional Japanese buildings and nature, these might suit you. If you want the kind of place where the hotel is your destination and you will be happy staying inside, you'll be happy anywhere. I guess I'm trying to say that "onsen town" does not = "picturesque, traditional small town." Only occasionally can you find such a place.

yes, I think onsen town = not picturesque and not traditional.

Thanks again KimJapan and mrwunrfl. I want to combine some city time (wan to check out Hiroshima and love Tokyo)with smaller town time (I loved Takayama and Kurashiki's canal area from my last trip). I don't think I would like the more typical onsen town you described except maybe for one night. But in looking up Gero I found Yunoshimakan which looked like the type place I was looking for but maybe the pictures are misleading.
Yamanaka looks interesting and someone said it was nicer than Yamashiro.
Can you suggest other towns in the mountains that I might like that would also ahve pleasant old style ryokans and/or rotenburo? Also does this mean I should skip places like Matsuyama? And places like Hakone and Beppu etc. Thanks again.

Also any other towns on the Sea of Japan side you'd recommend?

Yunoshimakan is probably a nice place to stay.

On the San-in side, Hagi and/or Matsue would be nice places to visit.

I just took the super-jet ferry from Hiroshima to Matsuyama. Tickets are about 6800 Yen each. The ride on the inland sea was a highlight of our trip -- it is gorgeous.

Matsuyama is a big city not a country town. Mrwunrfl is right that the Dogo Onsen is lovely. The facade of Matsuyama castle is being redone but you can still go inside. We just strolled the grounds and enjoyed the view. The street cars are easy to navigate; if you decide to go I can give you more info regarding stops.

We also found Beppu lovely. The sand baths and onsens are great and the gardens around the hells (the 5 we saw) were fantastic.

Kanazawa, Beppu and Matsuyama were not overcrowded with "foreign" tourists last week.

I wonder why you are returning to Hiroshima and not staying in Miyajima?

Shirakawa-go was interesting but the 4 hours we spent there was just the right amount of time for us. It was very touristy but perhaps if you stay overnight it could feel different.

moxie, I'm happy to hear that you enjoyed Dogo, Matsuyama, and the trip across the Seto Nai Kai.