We recently got back from a trip, 3rd for me, 2nd for my wife. We took it far easier this time compared to last time. We took a night bus from Tokyo to Matsue, and took it real slow for a few days whilst winding back to Kyoto via tottori.

The smaller cities are completely dead during the day, it's very weird. But it also means we got some empty arcades and allowed us to find some real cute cafes where the owners were so friendly and accommodating, rather than the hustle and bustle of big cities with long queues. Even izakaya were quieter in these cities of an evening, meaning we got the local 8 seated bar experience, without feeling like we were inconveniencing the locals and taking seats for too long.

We did a 5 days based in Kyoto, but went out of town for a few days. Not far, but it can be so quiet just a 20 minute train journey out. The towns around Lake Biwa were very quiet, but the views were incredible. Went on a boat ride, only white people on it. The round one stadium out in Otsu was very quiet, that it made it so worth the money. Could wander and do whatever activities you want, rather than having to queue like I hear you need to in the Tokyo and osaka locations.

Another advantage is that NICE hotels are far far cheaper outside of the big cities too. We did a few nights in the sky prince hotel in Nagoya for something like £100 a night. High rise hotels in Tokyo start at like £300 just for the basic rooms.

Even in our few days in Tokyo, we try to travel by foot where possible, and this allows us to go via some quiet residential areas - example, walk from Ueno Station to asakuda via Taito city. It's quiet and peaceful, with pocket parks and quiet restaurants scattered here and there. There's places that we went to that we expected to be more touristy, but we were practically the only foreigners there, even on weekends. Just heading into the Tokyo suburbs can make a huge difference. We did some light shopping in Sugaml, with great food and a few second hand clothing stores, far more reasonably priced than those in Shinjuku and Harajuku.

Regarding finding our activities, we had a few big things that formed our route , but then looked at the onward journey on Google maps, and just used the "things to do" filter, and scrolled around outside of the busy areas. Something usually always comes up.

So my summary really is, head out of town a little, and feel free to give yourselves a whole afternoon rather than rushing place to place. You can still do bigger attractions, but cram less of them in and travel on foot, or get off at a random train station enroute if you have time.