I love Japan, I've been to Japan twice and am always thinking about going back. This wiki page will broadly document what we did on both trips, and highlight some recommendations, particularly where we found seasonal events or strayed from the beaten path.
Tokyo/Osaka/Kyoto are great, and you should definitely spend some time in some or all of them if its your first time in Japan, but I really encourage going further afield. We've found a number of unique spots that aren't on the usual tourism checklists. It can be a little scary straying from comfortable cities, but anywhere remotely touristy will accommodate you in some way at least, whether you speak Japanese or not.
About our trips
Winter 2016 - Two weeks
We hit a few tourist spots but tried to not treat it like a checklist and avoided staying in one place too long
On this trip we stayed in
We stayed in Japan for Christmas and flew back on Boxing Day
Spring 2018 - Three weeks
This time we went in spring to see the cherry blossoms and planned a trip where we could follow them from the south (Kyushu) up as far as Sendai
This time we made more day trips out, particularly in Kyushu where we treated Fukuoka as a base
25th birthday
Recommendations
Tokyo
Day trips
Ghibli Museum -
Odaiba - Walk across the bridge (closes @ X:00, we had to get a bus back), giant Gundam, we went whent he original one was there, but I'd love to go back and see the newer one
Nara
Nara's a good day trip spot from Kyoto or Osaka
Attractions
Giant Buddha
Deer - so distracted we forgot why we were there
Kyoto
Osaka
I'm kind of indifferent to Osaka
Nagoya
We only stayed in Nagoya for a couple of nights, it was a convenient spot to travel up to Takayama matsuri (the train ride was long, but the views were great) and I had a few food recommendations from my Japanese teacher
Food
Yamachan
pork place...
Accommodation
Book...
Sendai
Day trips
slope car
lotsa islands place
Hiroshima
Food
Attractions
Miyajima - famous torii gate in the sea, deer, supposedly less polite than Nara's, but I found them to be much more chilled out
Peace Museum
Accommodation
Day trips
Okunoshima (Bunny Island)
Kinosaki
Fukuoka
Food
Raumen Stadium - Hakata style, tomato ramen
Day trips
Kumamoto - castle, destroyed by an earthquake
Beppu - 7 Hells/Jigoku, we made the mistake of not trying the puddings at the first one thinking there'd be more opportunities, convenient buses to get around
Kanagawa
Kanazawa
We visited Kanazawa for the castle garden while the blossoms were out, and only stayed a night, but filled the day with a number of museums
Attractions
Phonograph Museum - Regular talks going through a number of vintage phonographs, accommodated us with print-outs of the talk in English. Happened to be there on a Sunday too, when they have a demonstration of a self-playing piano which was a treat (although this lacked any English)
Gold Leaf Museum -
Sweets Museum -
Food/Drink
Oriental Brewing - A micro-brewery and pizza
Accommodation
Omatsuri (Festivals)
Another consideration we make when we visit Japan is seeing if there are any festivals or anything going on while we're out there and planning where we are around them. Exciting to be immersed in Japanese
Kyoto (Arashiyama) - Lantern Fesitval
Kyoto (Sakura) - obakeyashiki (haunted house)
Nara
Beppu - Didn't have time to get involved, saw some mascots but we were there to see the Hells
Takayama - the town is known for its sake and a number of shops have a sake tasting where you buy a cup and keep filling it up from the fridge, and take your cup home when you're done, the festival itself was amazing, massive intricate floats, and puppet shows
Hanami Tokyo
Chain Food
GoGo Curry - I see Coco Ichiban gets a lot of love from my fellow weebs, but I can't eat their curry sauce due to allergies, but GoGo Curry do some
Ichiran Ramen - Individual booths, served tonkotsu (pork bone) ramen made to your liking. Personally I like my broth rich and my noodles firm