I read an article recently about how Tokyo, Kyoto and Osaka are heavily overtouristed, and the problem seems to be getting worse, fraying the nerves of both visitors and locals.
I hope people could consider getting off the beaten tourist path a bit and going outside the "golden highway" between Tokyo and Osaka. There's plenty of locations in Japan that are absolutely beautiful, fun, and culturally enriching, which have very, very few foreign tourists (or any tourists at all, sometimes). All of the best experiences I've had in the country were away from the crowds.
Here's some ideas, and if other people wanted to contribute some, maybe that would be cool and helpful to some folk :)
Kyoto has plenty of beautiful temples, shrines, and gardens. But also plenty of tourists. Hirosaki and Kanazawa both have some excellent temples, shrines, and gardens, along with castle ruins at both. They're far less crowded and the people are very welcoming.
For nightlife, Sapporo in the North and Fukuoka in the South, both have some great party areas with packed bars and excellent brew on tap.
Day trips to Mt. Fuji are nice, but Mt. Aso in Kyushu (active volcano with huge, green caldera you can take a ropeway up to see), Mt. Hakodate in Southern Hokkaido (the view from the summit is the most stunning in the world at night), and Mt. Haku in Gifu, which is quiet yet beautiful.
If you really want to experience some of Japan's remote and unspoiled beauty, any of the cities and towns dotting the Sea of Japan ("other" coastline) get practically no visitors from outside the country (aside from Niigata, and even that place is underrated). Tottori has amazing sand dunes with all the associated fun activities (sandboarding, paragliding, camel rides, and a local legend about a cursed woman).
Or practically anywhere in Shikoku, which is basically the everyday Japan, without the hype. The prefectural capitals here all have museums, nightlife, attractions, and restaurants (geared towards locals instead of tourists, so higher quality and lower price). The towns and villages are full of friendly and interesting people, and the air is often so fresh it's intoxicating.
I definitely don't want to slam Tokyo or Osaka; I love those places and everyone needs to check them out at least once in their lifetime. But dedicating part of your vacation to seeing some of Japan's less instagrammed places could be a really awesome experience, too :)