Japan Itinerary (mostly western area)

It's me and my friends' fourth time to go to Japan now, and we want to focus on the western part of Japan. Our trip will last 10-12 days and our airport will either be in Nagoya or Osaka (these are the only 2 airports where our airline stops). We need some help with the Itinerary. We will start off in Nagoya and Travel to Takayama, but after that we're not sure where to go. We already went to Osaka Kyoto Okayama and Kurashiki, so this time we want to go to the regions of Tohoku (to visit the Ginzan Onsen and Naruko Gorge), Shikoku, and Kyushu, specifically Yakushima.

We're not sure how travel will go, is the JR pass still useful? Are there any recommended (affordable) local tours available? Thanks a lot!

I recommend going to Hagi. Rent a bicycle and explore the area.

http://www.japan-guide.com/e/e6150.html

We will start off in Nagoya and Travel to Takayama, but after that we're not sure where to go. We already went to Osaka Kyoto Okayama and Kurashiki, so this time we want to go to the regions of Tohoku (to visit the Ginzan Onsen and Naruko Gorge), Shikoku, and Kyushu, specifically Yakushima

Those all seem like great places, but it may be a bit much to pack into just 10-12 days, especially if you plan to combine the Tōhoku region (in eastern Japan) with the western regions.

It's certainly possible to do either western or eastern Japan from an entry point via Nagoya, or even both if you have a longer holiday period, but for less than 2 weeks it might be better to focus on one part or the other (and save the rest for a future trip).

Building on Hagi's good suggestion, a thorough exploration of the Chūgoku region may be well worth considering. You've had a taste of it in Okayama, but now you can venture farther west and north to enjoy even more of the area. I spent several days there last year before moving on to Kyūshū (easily accessible from the region) and I'm quite eager to go back.

http://www.japan-guide.com/list/e1106.html

Cheers.

We're not sure how travel will go, is the JR pass still useful? Are there any recommended (affordable) local tours available?

If you're travelling extensively in western Japan after March 2015, check this out:

http://www.japan-guide.com/news/0031.html

One of those new/improved passes might be useful for your trip.

Thanks a lot! I didn't know about the new train passes, it looks like it will indeed help a lot :)

I also checked out Hagi, and it's indeed a wonderful place. We will take your suggestion and focus on 1 or 2 of the regions. Are there any other notable places to go to?

Also, I wanted to know what city is best to stay in, like which is the best location to make our "home base". Thanks!

If you happen to travel to Japan on a Oneworld carrier and you still plan to combine Tohoku with Western Japan, you might want to have a look at this special fare by JAL.

http://www.fr.jal.com/world/en/visittohoku/

Since you have limited time, you probably don't want to waste the best part of a day in the Shinkansen. ;)

I also checked out Hagi, and it's indeed a wonderful place. We will take your suggestion and focus on 1 or 2 of the regions. Are there any other notable places to go to?

Doing Hagi-Izumo-Matsue-Tottori-Amanohashidate-Osaka before flying home sounds nice (but be very careful with planning, trains are relatively slow and infrequent over there).

Having a "home base" is a bad idea for the kind of trip you want to do. Book hotels in the places you want to visit. You will have to go there anyway, and you really don't want to have to backtrack.

I'm a bit confused...
You write you "want to focus on the western part of Japan"..."so this time we want to go to the regions of Tohoku"?? You still haven't seen a lot in the area.
Also, when are you traveling? Especially for the Tohoku area, the season matters a lot. You mention you want to go to 4 different areas - that is too much for such a time span, unless you want to waste a lot of time rushing on trains. If you want to see Takayama, that is one good famous area. Nearby Inuyama is nice as well, and if you want to try hiking the old Nakasendo a bit, there is the Kiso Valley.
There are a number of great places in the west as you mentioned though, many largely off the beaten trail. Kotohira in Kagawa has a great shrine on a mountaintop - a trip you will never forget:
https://www.youtube.com/watch?v=ley9rVIewoQ
Onomichi makes a nice visit, especially the Kosanji temple:
https://www.youtube.com/watch?v=97Q5EjEOXI8
You also didn't mention Nara in the Kansai area, which is a must-see city.
Farther down is Hiroshima/Miyajima, which are excellent places. Iwakuni is also a good day trip; the bridge and mountaintop castle are great:
https://www.youtube.com/watch?v=0COOZXi66mM
Someone mentioned Hagi, which is very enjoyable, and don't miss the Akiyoshido Limestone Cave in Yamaguchi as well.
If you really want to get to Yakushima, which is quite time consuming, your time in Kyushu will be limited. You might concentrate on just a few areas, like Fukuoka, Nagasaki, Kagoshima, and Kumamoto if you still have time.
For Fukuoka, see this site as a good guide:
http://www.thejapanfaq.com/fukpic.html
There are also many useful videos to give you a preview:
https://www.youtube.com/playlist?list=PL7LcPcmoSg-j4RLa6iC7ayvBAbOn8-0...
Look into a Fukuoka Tourist City Pass also:
http://yokanavi.com/access_tourist_eg
One superb sight is the Nanzoin temple, truly astonishing and totally free:
https://www.youtube.com/watch?v=lT4VQFmHFyM
In terms of history and varied points of interest, Nagasaki is the best city on the island. It is worth a couple days and Gunkanjima, while it takes 3 hours, will blow your mind.
http://www.ngs-kenkanren.com/eng/
http://www.at-nagasaki.jp/foreign/english/
http://www.youtube.com/watch?v=QdWRyHGW3rk
Be sure to see Mt. Inasa at night if the weather is clear, and try the Nagasaki chanpon and saraudon! Also the Koshibyo temple is an often overlooked shrine that is quite unique in Japan:
https://www.youtube.com/watch?v=Mu_JnkVInTU
Kagoshima is great to see the live Sakurajima volcano, hiking, and hot sand baths such as on Ibusuki. Plus the Senganen garden has a superb backdrop view of the bay and the volcano. See:
http://www.kagoshima-kankou.com/for/
https://www.youtube.com/watch?v=LxDmLuq6ssI
https://www.youtube.com/watch?v=lpnDK_Wux9Q
In any event, you need to think about travel time more. Look at hyperdia.com to see rail travel times, and adjust your itinerary.

Hi Ken! Yes we realized that the time might be too short so we decided to just focus on one region at a time like I told Firas and Diego de Manla :) Your suggestions all look like amazing places to go to! We will definitely make a new itinerary with all the suggestions we got!