Trip to Japan in late June 2025

Thanks ORDTraveller for your insights. I could modify my itinerary as follows:
1. Spend 4 nights in Kyoto doing the day trips to Nara and Hiroshima besides local sightseeing (May think of spending one night in Hiroshima)
That still leaves 2 nights - Could I fit in the cooler Sapporo city into my itinerary and fly out from Sapporo back home instead of Tokyo ?
Well, we will be first time visitors to Japan, so dont have too many fixed choices, except that we (must) want to experience traditonal Japanese hospitality and cuisine - tea ceremony, teppanyaki - anything else ?
Easy nature hikes and temple/garden visits are also on the list
Need advice on the must do/see/visit/experience things in Tokyo city.
Also will be looking at a day trip from Tokyo
Sumeet

Rather than add another city for only two days, would you consider extending your time in Tokyo and Kyoto by a night each and adding day trips? From Tokyo, Nikko, Kamakura, and Kawagoe are all very worthwhile. From Kyoto, you hardly have any time there if you are also going to Hiroshima and Nara. Between Kyoto and Nara, Uji is worth a stop or a separate half day trip.

Don't miss a day trip from Tokyo to Nikko.
Kyoto and Nara are worth 4 nights
Osaka and Kobe are worth short visits. I remember Osaka Castle.
Himeji Castle is great, it was in a James Bond movie.

I agree you should look at extending your time where you already are. You are barely spending any time in Kyoto it seems as you are using 2 of the days for day trips. Also, it's not clear, does your 4 nights in Tokyo include your arrival day? If so, I am assuming your first day will be pretty much shot after arrival, jet lag, navigating a new city, checking in to the hotel, etc.

Mt. Fuji is absolutely worth it if you can see it but you are correct it can be hit or miss and very often miss. The months with the best chances to see it are usually the winter months when the air is drier. That said, of course it is still possible you may get a good day. I assume you are thinking of doing it as a day trip from Tokyo. I would check the weather the night before and the morning of when you are planning to go. There are also webcams you can check to see the current visibility and then decide if you want to go or not. You might also be able to see it from the shinkansen on the way from Tokyo to kyoto.

Also, something to keep in mind, it seems you'll be there during rainy season so just keep that in mind when planning your days and activities.

In that case, probably best to keep Sapporo for another trip and maximise time in Tokyo/Kyoto. Will be looking at all your suggested day trips from both cities. Thanks a lot!
Also have decided to stay a night in Hiroshima and do a day excursion to Miyajima.
Need advice regarding the 7-day JR Rail pass, given the following facts:
1. our trip is at least 9 nights (maybe 10 also) and I will be flying in and out of Tokyo (BTW we are from India and will be travelling from/to Delhi so can try for return flight from Osaka too - will that offer us any advantage ? pls suggest)
2. Our itinerary will most likely be : Tokyo 4 nights (+2 day excursions)- Kyoto 4 nights (+2 day excursions) - Hiroshima 1 night (+excursion to Miyajima) - back to Tokyo (or Osaka) for return flight
3. We will need the JR rail pass on the last day to travel to Haneda (or Kansai) airport
Given these facts, when do you suggest should I activate the JR pass ? If I do so after the first 3 days, I will need to use the SUICA card for local Tokyo travel - does the Suica card cover for local excursions from Tokyo e.g., Nikko, Kamakura etc ?

You will not need a JR pass with your route. Especially not if you are able to fly out of Osaka.
By the way, if you are able to fly out of Osaka, I would reshuffle the trip and do Tokyo - Hiroshima - Kyoto. Osaka airport is easily reached from Kyoto, 80 min by direct Haruka train. That way, you won't need to change hotels once more.

Oh, and Mt Fuji views in late June are indeed unlikely.