What to do in Kyushu?

Hello everyone,

I have been to Japan before but never left Honshu.

Now we want to go to Kyushu for a couple of days with a JR Pass. We will come from Hiroshima/Miyajima and definitely want to see Nagasaki. Sadly, the Gunkanjima tours are all booked :( -
We will leave after 3 days from Fukuoka to fly to Ishigaki jima.

What's your advice on what we could do during these days?

Thanks for your help!

Yes, Nagasaki is a good place to go. You can also go to the bottom of the island (Kagoshima), head to the mountains, or enjoy the hot springs in Beppu.

Yufuin can be done as a day trip from Fukuoka; it's a lovely hot spring town and has a shopping street featuring traditional buildings.
Closer to Fukuoka is Nanzoin, which has a temple featuring the world's largest bronze statue...which almost no one knows about! Less tourists, and the temple is very quiet and serene. It's about 20 minutes by train from Fukuoka.

sq,
You must add that Nanzoin's Buddha statue is the largest of the "bronze" "reclining" Buddha statue :) Among the top 20 largest in the world as "reclining" Buddha statue.

With three days, this is what I recommend.
Day 1
Train to Kumamoto. See the castle and park. Plus museum. Eat lunch here. Train to aso. See nature along the rail. Have a tea break at some station.
Night at yufuin, beppu or Kurokawa

Day 2 tour about the onsen town.
Train to Miyazaki. See aoshima, and udo jinja. Go up and down the sanchirin Coast.
Night here.

Day 3
Head to Kagoshima. Go to ibusuki for the sand bath. sightsee around ibusuki or Kagoshima. Eat at juan near the main station. Either night here or take a late shinkansen back to hakata station and night at one of the hotels near the station

You don't give any info on your interests, which would help a lot. Plus if you have a rail pass or not - that would add to your savings. If not, consider getting a JR Kyushu Rail Pass.
The suggestion of seeing Nanzoin is excellent. It is a must see place that you will never forget - and on top of all that, it is free!
https://www.youtube.com/watch?v=lT4VQFmHFyM
For Fukuoka, there are many open parks, shopping, seaside historical areas, and urban neon. 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...
In terms of history and varied points of interest, Nagasaki is really the most interesting city on the island. It is worth a couple days to see the city, and another day to see areas nearby like Shimabara/Unzen or whatever interests you. Gunkanjima, while it takes 3 hours, would have been well worth it.
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
The area around the Aso crater is still closed, so unless you are driving to see some other good places near there, you can more effectively use your time elsewhere. Same thing for Miyazaki - more pain for less gain. Takachiho is nice, but very time consuming to get to.
Kagoshima is easy to get to though and 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
Lastly if you have time, Kitakyushu has a few sights of interest also. It's Kokura Castle is one of the better ones, the view from its Moji wharf and preserved buildings are quite historical, and the view from atop Sarakurayama is one of Japan's best and rarely mentioned:
https://www.youtube.com/watch?v=Hl1pCW9Ibbk
For comprehensive info on Kyushu, see:
http://www.visitkyushu.org

Usuki Stone Buddhas is also worth a visit.
http://www.japan-guide.com/e/e4742.html
Usuki is located south of Beppu. Most buddhas in Japan are made out of wood or metal. These stone buddhas are believed to be some of the oldest ones and are carved out in a cliff.
Visitors can borrow a bamboo walking pole to help navigate the climbing walking trail and stairs. A unique setting from where you have a beautiful view over rice paddies and a pond with lotus plants flowering in the summer.

Thank you very much for your helpful advice! It is good to know that some areas will be closed or in break during September.

The travel advice also helps a lot because even with a JR Pass, you never know which place you can actually reach in time and without further annoyances like taking private trains or busses.

Thanks everyone!