I just got back from my second trip to Japan a few days ago, in my personal experience I really did not like Kyoto. Overcrowded with tourists, pain to get anywhere because the public transportation sucks, and the famous temples arent close to eachother so you have to pick and choose. Not to say its not worth going as some of the temples I went to were absolutely beautiful, but I ultimately felt I could have used my time better. Kyoto highlight is some relatively famous temple I passed on my way back from that famous high up wood one that had a very ornate gold set up on the inside that amazed me, that and randomly coming across the Tamako market market and the exact spot on the river from the first scene of Tatami Galaxy (which are right next to eachother)
If you want to really get a taste of what Japan is actually like with a focus on seeing very Japanese looking buildings/going to temples and shrines I would recommend checking out the Shikoku henro and finding some places to go along those lines, I recently did a couple days of hiking in Kagawa and the nature was beautiful, the temples ranged from being very cool to downright mystic, and because I was hiking it wearing a white shirt (pilgrims have a specific white shirt sort of thing they usually wear but a normal white shirt is fine) I had a guy pull over while I was hiking and give me a multiple mile ride from near the top of a mountain to the temple I was going to in the city. Another notable encounter was at the entrance to the hike up to the temple at a different mountain I had an old lady call out to me and give me free tea and snacks along with letting me sit on her front porch for a bit. As
>>108471 said these people really appreciated the fact that I can speak decent enough Japanese and the fact that I could opened up 'real' Japan to me instead of getting the surface level that comes with not being able to properly talk to most people, even just trying is better than retreating to English. Doing the actual trail can be alot, but even the cities I stayed in while hiking were a very different experience than the big touristy ones and the temples in the cities are still great.
If you want to do Fuji you should check if you are going in the right time of year, while you are in that area I would recommend a ryokan in Numazu, even if you arent into love live its a neat place to stay and really close to Fuji.
I didnt find Akiba as disappointing as others but I think part of it is going in acknowledging that all the world knows about it and itll forever be tainted by idiot foreigners who treat Japan like a zoo, there are still good places within it and its still alot of fun to walk around stores once you get a good idea of where everything is but it is always annoying to be sitting there playing kantai collection and seeing some normo white couple in gaudy clothes gawking at people just trying to game. I have had positive experience with westerners in Akiba though, this most recent time I ran into a guy in a maid cafe who said the building was the first one he had went to 7 years ago when he first went to Japan, the place has changed since then but the building was also where I went to my first maid cafe the first time I went to Japan last December. Maid cafes are very fun if you can speak enough Japanese. Animate's outside of Tokyo are pretty fun to go to, the Hiroshima one was surprisingly big and funnily enough right next to the atomic bomb peace park.
Other thing is there is only one channel that consistently plays anime and its usually only from 10pm-1ish but its very worth planning around doing. Havent been watching the show but watched yuri is my job from my japanese style box hotel in Tokyo that was just big enough for the futon.
Favorite thing is hard to say but if I had to choose something I'll go with being very drunk in a maid cafe/girls bar sort of thing with a friend who was also in Japan, listening to drunk salarymen do an intentionally terrible job of singing gundam songs in karaoke, playing uno with the girl behind the counter and some old guy who was actually really good at english. Yashima-Ji and Yakuri-Ji are also a great experience. They are both on top of mountains right next to eachother, from Yashima-ji you can see all of Takamatsu, Okayama prefecture on the other side of the water, and from the other side of the mountain the Yashima-Ji mountain. You walk straight down Mt Yashima to a small ruralish town by the water then back up to a temple with a very strong spiritual feeling to it.
Oh and one last thing, DO NOT go to shibuya, shinjuku, or harujuku. Just dont, they suck. The area is only worth going to for Meiji Jingu, the one park garden of words is set in (which I sadly didnt have time for this trip), and Harajuku gamers (only worth going to if you like love live)