What are some scenic sites or nature spots in Japan that you had long heard about, but disappointed you when you saw them for the first time?

None so far.

For me was the opposite, all the travel places live up to the hype. Maybe just when it's too crowded and the long wait in line, it was quite tiresome and stressful (places like Universal Studios, Disneyland, etc could be so packed and the line for attractions are long on popular rides).

Some places could be very underrated too. Some beaches in Okinawa was mind blowing beautiful for me but wasn't that really heard of.

Amanohashidate itself is beautiful, but the amount of trash floating in the bay around the sandbar when I went was disheartening.

Matsushima. Got roped into a bus tour that took us there. It was nice for sure, but the bus didn't take us up the hill where apparently the view is far better.

Many Japanese had raved to me about Manza beach in Okinawa, but you could randomly drop a pin on just about any beach in Australia that would relegate Manza to the ranks of meh.

Tokyo. I find it quite heartless as a city compared to Osaka

Mt. Fuji. as much as it is beautiful, it's also a tourist trap. Camp sites around during peak camping season looks like there's a music festival there everyday. climbing the mountain is also something. imagine how bustling new year's eve is, but on a mountain. the experience is not serene but stressful.

Most of Kyoto. Beginning 35 years ago. There are a few nice spots here and there but most of it is generic or substandard city, with shoddy buildings, poles and wires, car parks, ugly signage, etc. In fact, what has been done to it is nothing short of criminal. It would not compare in any way to a beautiful city in Europe which would at least have a large, attractively-kept city centre as well as other sites around.

Maybe just when it's too crowded

This was my experience too. I love Japanese gardens, and was excited when I finally got to Kanazawa to see Kenroku-en, one of the "Three Great Gardens of Japan." But I knew it was going to be trouble when I got there and saw the pack of tour buses out front. Huge groups of people swarming everywhere in the garden. Want to see the pond? You need to fight your way through 300 people holding up iPads over their heads to take photos, rowdy children (and adults too), selfie-sticks, people loudly having video chats via their phones... it was awful. The garden is beautiful, but gardens are meant to be tranquil places to enjoyed peacefully. It was a miserable experience and I left very disappointed.

Hokkaido. I was told it was large and beautiful but I had just come from living in Iowa, so it was just more of the same. Maybe I should go back after living in a crowded Kanto city for awhile; might change my perspective.

The "Seven Hells Onsen" (hot springs) in Beppu.

They're actually seven separate mud pits that had something unique about them generations ago, but are now simply mud pits which you pay big money to travel to and look at from far away while understanding that there was something unique about them generations ago.

Also Kyoto. Everything about Kyoto is underwhelming except for the prices and the whinging of locals, which are quite overwhelming. I don't know how long they can milk the rubes until people realize it's just the pyramids of Giza with fewer touts, less public transport, but more electric poles and hanging wires and much more whinging.

Kawagoe. Needs pedestrianisation and some rules about advertising and signage. The route from the station also needs to be marked.

Kyoto is choked with traffic because the rail network doesn't convey people to tourist attractions. This results in bus/taxi jams.

I knew Kinkaku-ji would be rammed, so shuffling along in single file wasn't a problem. I think most people are aware that tourist sites in Japan are going to be busy.

In general, the crowds don't bother me. People generally flow like water in Japan. In places like Takeshita Street and Nakamise Street, the crowd adds to the vibe. Just be careful of people walking out of a station and then stopping to get their barings, not realising that fifty people are behind them not expecting to suddenly stop.

There are plenty of places you can go that are not full of tourists. Japan has lots of shrines and temples, many smaller ones being wonderfully atmospheric. Uguisudani is smack in the middle of Tokyo and famous for its love hotels. But I stood in Jomyoin Temple at twilight, surrounded by really old graves and sculptures, the sun setting, shadows lengthening, absolute silence, nobody else there. It was mesmerising. Kaneji Temple was a short walk away, also atmospheric. If you want a solitary experience, scan Google Maps, check areas around stations and do some research.

There are plenty of Japanese gardens too, so do your research and head for the less well known ones that are a bit further out.

Agree with Moonraker

Nagasaki peace park

Overcrowded with noisy, rowdy chinese tourists ( one kid peed into the fountain)

Beppu Geiser. They block it from possibly reaching four floors in height.

Gran Shinkansen was great three out of four times, but the fourth time had 5 drunks because the alcohol comes with the ticket. They ruined the whole trip from Shinhakodate to Tokyo. They looked like a pachinko crowd.

Invalid CSRF: What is this message?

Hariyama Bridge in Kochi city. Don't fall for it. It's three meters long next to a sidewalk.

Sapporo Clock Tower. Just a small white wooden building with, you guessed it, a clock on top of it.

Ijinkan in Kobe. Just another wooden building with a chicken weather vane on top.

Not just Japan, but basically almost every famous landmark is, at best, pretty much like all the pictures I have seen. If flooded with tourists, as most are these days, it's even worse.

I don't make a special effort to see all the famous sites. There are always tons of completely overlooked areas of natural beauty and cultural interest where I ask myself, "Why isn't this place famous?" Sometimes they become famous and ruined by tourist hordes like everyplace else.

Finding some little spot with a few engaging locals will almost always be more memorable. For natural beauty, Japan is filled with stunning waterfalls, for example, that hardly anybody visits.