My response to this Quora question.
There are several things you might want to consider, so it’s probably best to make your own decision after thinking things through. Note that I’ve mostly been to Japan during the summer (July/August) so I can’t comment too much on June and September.
First of all is the weather. Tokyo, at least for me, gets intolerably hot during the summer. If you’re just visiting, then it’s likely you’ll be taking a lot of public transportation, which will involve walking to and from train stations, which, depending on your destination, might be a long walk1. And walking outside in Japan means dealing with the sun, the humidity, lots of sweat, etc.
Also keep in mind that a lot of places get crowded during the summer (especially late July and August) because that’s when summer break happens, which means suddenly at a lot of attractions you’ll see a big increase in the number of people—especially kids. This is particularly true for places like Tokyo Disney Land. (For this, there’s a convenient calendar predicting the expected number of visitors per day; it’s in Japanese, but you can click on “前月” to navigate to the previous month, and “次月” to see the next month. Just look at how red August is! There is also this article that discusses some visitor patterns for Disney Land and Disney Sea.)
There are some more local patterns in the number of people that are noticeable during the summer. If you want to visit the atomic dome, you probably don’t want to be doing that on August 6. There are also anti-Yasukuni protests that happen each year on August 15, which are fascinating to go to (and incredibly well-planned and safe), though that’s probably not the day to go shopping in that area.2
If you’re looking to buy any clothes, then remember that sales usually happen for clothes that don’t match the current season; though conversely, these are also older, so the newest items will be those that fit the season.
There are parks/gardens in lots of places in Tokyo, so it isn’t necessary to travel too far, though you might find that e.g. the parks in Kyoto have a different aesthetic. Also do remember that in summer, there are a lot of mosquitoes, especially in parks with ponds, just waiting to get you as you sit down in the shade to enjoy the plants and koi swimming around …
For food, there are restaurants everywhere around Tokyo, so you probably won’t eat the same thing twice even if you visit just a small part of Tokyo. One thing to note: Japan isn’t a very vegetarian/vegan-friendly place, so good luck trying to find a dish that isn’t trying to kill you.
As for onsen, I’m not sure going to a fancy place out in the countryside with natural springs and a five star rating is really worth it. I’m probably less sensitive to these things than most people, but I certainly don’t see much difference in going to a local public bath that’s a 10 minute walk away and costs 500 yen versus paying 10,000 yen a night to stay in some fancy hotel. And I suspect that for a first-time visitor, there is an even stronger case that a fancy place isn’t worth the cost: probably the most novel thing about the experience is the fact that the bath is public, which is an experience you can get at even a cheap place. Plus, there’s a chance you’ll hate it, so going to a cheap place is safer. I will mention that I did go to the Ooedo Onsen a few years back, which was nice enough, but costs 2,480 yen for a day (i.e. just during the day and not spending the night). It’s not just an onsen though, and it does have some extra things like a footbath with doctor fish as well as a matsuri-like atmosphere inside, which might appeal to tourists. It’s also conveniently in Odaiba, which has some other neat places to visit (including what appeared to be an obscure condom shop that I once spotted …).
Also you should keep in mind that your friend might only let you stay with him during a narrow window, which might constrain your choice of when to visit (i.e. if you only plan to visit for a short period, then you might have to stay exactly during the time when your friend allows you to; if you plan to stay for a longer period, then you have the flexibility of staying during the time immediately before or immediately after when he allows you to stay with him).
Of course, if you’re only shopping in department stores that are connected to the train stations, then this won’t matter, but from your description it sounds like you’ll be spending a lot of time outdoors.↩
I should probably write about my experience of going to the protest at some point. For now I’ll just say that observing the left-wing versus right-wing (with the police being sandwiched between the two) dynamic playing out in front of you is really interesting, especially since if you live in Japan, you don’t see a lot of people getting worked up about politics.
Also, the protests are almost never covered on television news (you can find a lot of YouTube videos though) so it’s kind of a thing that most citizens don’t even see.↩