Do you like nature and/or gardens? These are the things I probably enjoy most in Japan (itfs a toss-up with the foodc). And in fact, some temples and shrines are among the best places to experience these things. I pick my temple and shrine visits mainly based on what the grounds are like, rather than the structures or historical artifacts. (For the most part, the most famous shrines and temples in Kyoto are not on the list of ones I would recommend for nature experiences, though.) There are also good places to hike in Japan if you like that sort of thing. Some of them are readily accessible by public transit, although this can require considerable research.
Staying near a train station is definitely the way to go if you want to simplify your trip. In fact, I tend to favor hotels that are directly connected to a JR station (I always buy a JR pass and get very good use out of it, as one of the other things I greatly enjoy in Japan is recreational train riding). Although the rainy season in Japan typically starts in early to mid-June, it can rain quite a bit in late May, and it can also be beastly hot. So it is nice to have a short and sheltered path to and from your hotel. Of course which train station you want to stay near depends on a number of factors. Sometimes it is easier to pick an obvious central location (Kyoto Station or Tokyo Station) and then plan your trip based on what places are easy to get to from there. This is gbackwardsh in most peoplefs thinking, and so is my basic approach for buying a rail pass (I look at the various passes and where I can go with them, then make up an itinerary that uses one or more of them effectively). But it works for mec There are just so many things to do in Japan that you donft necessarily have to start with a prefabricated Top Ten list designed for a gtypical touristh and then figure out how the heck to get to all those places.
You are very unlikely to get lost in Japan especially if you have cell phone data service and Google maps. Or download maps before you go, or pick them up at tourist information centers. Also, note that Japan is very safe for tourists (as long as you have a modicum of common sense), and people will often help you if you are lost. (Stand somewhere looking at a map with a befuddled expression on your face, and typically in no time some kind native will ask if you need help.)
Some of the most popular tourist sites in Kyoto are somewhat of a pain to get to if you use public transit, but if you use cabs it becomes quite easy. Cabs are always waiting at major train stations, and at popular tourist venues. Whatever you do, try to avoid taking buses to the major tourist sites in Kyoto, although for some it is often recommended that you get a bus day pass (one of the worst pieces of advice, for most people). Cabs are much less necessary in Tokyo because they have an excellent train system (subways plus a few aboveground JR lines). Learn about IC cards if you havenft already.
If you are planning to hang around Tokyo that many days and donft plan to take a lot of day trips, you might get good use out of a Grutto Pass, which covers many museums and also some other types of venues in the Tokyo area. I have gotten one a couple of times in the past, but typically I donft spend enough days in Tokyo to get enough use out of it. Note that the information online now is for the 2022 pass that expires in March. Presumably information on the 2023 pass will be up before you go.
https://www.rekibun.or.jp/en/grutto/If I have any more general advice, it is to do a lot more basic research on places you might enjoy going to. Japan Guide is a terrific resource for that. I also like Time Out Tokyo, for Tokyo:
https://www.timeout.com/tokyo
