JRPass

Hi there,

Firstly, the 21 day nationwide Japan Rail Pass is valid on all JR lines across all Japan, including those you'll find in Kyushu. Here's a sample itinerary that you can use to get to Beppu from Fukuoka with a JR Pass.

Onto the question of Hotels. This is a pretty big topic, and is really dependent on a lot of factors. Hotels in Japan are in a constant state of change, so I recommend that you check tripadvisor first, and then have a look for the hotels you'd like on google or an aggregator like JapanTravellerOnline, or RakutenTravel. If you're looking for a boutique approach, then I'm a big fan of JapaneseGuestHouses.

That said (and I usually regret this...), I've stayed in and had a decent experience at the following low cost hotels (not ryokan):

• Hotel Vista Kyoto. Just behind the station - not picturesque, but ultra convenient, clean and cheap.
• Plaza hotel Tenjin (fukuoka). I like this hotel - it's close to where the action is in Fukuoka, clean and reasonable.
• Tokyo is a hard one - best to use tripadvisor here. For cheap and convenient, the Tokyustay apartment hotels have washingmachines, fridges and mini cooker facilities so you can really exist on a budget. Again, not wonderfully picturesque but practical. At the other end of the scale I really enjoyed my stay in the hotel Granbell in Shibuya last time I was in Tokyo, as always it really depends on your budget here. Possibly look in the Nakameguro and Daikanyama area for other ideas and trendy spots.
• For Hiroshima I recommend staying on Miyajima if you possibly can
• For onsen in Kyushu, how about staying at Kurokawa onsen? I personally much prefer this to Beppu and think it's well worth the price bump you may have for the shear experience of it. If not Kurokawa, then consider Kinosaki onsen on the sea of Japan coast of Honshu (nearest stop on your itinerary is Osaka).

Hope this helps!