I've just been planning my own trip to Japan and thought I'd put together a similar deal. I've chosen some good rated hotels that are near stations and also included a 7 day rail pass for Japan so the majority of the train travel outside of Tokyo (for which you can use the metro) is included. This is just an example, for a longer itinerary you can include the alps, Mt Koyasan and longer in Kyoto.
This is for March 2017 and based on 2 people.
You'll leave London and fly with the Italian airline Altalia arrive in Rome later that evening. You don't leave Rome until the following afternoon so you can have an evening and morning exploring Rome. I've included the Aurelis Art Gallery Hotel as this is centrally located for metro lines and also for a quick morning of sightseeing.
Leaving Rome you'll fly to Tokyo arriving on 22nd March.
Once in Tokyo you will stay at the Shinjunku New City. It's near the JR station and the hotel also offers a free shuttle. I've picked this hotel for my October holiday as it had good reviews and is also a good price. You can easily access many places from the station but you will also return to this hotel at the end of your stay so whether it's shopping, food, or Tokyo Disneyland you'll have plenty to keep you occupied.
Activating your railpass today you can head to Takayama where you will stay at the Country Hotel. Takayama is more rural and scenic and a good place to base yourself for visiting the alps, onsens, views of Fuji and getting out to the countryside.
You'll head by train to Hiroshima today. With plenty of history you can visit the peace memorial and also take the ferry over to Miyajima (included with your railcard). You will stay at the highly rated Parkside Hotel which is ideal for public transport access.
You'll take the short train journey to Kyoto today. This is one place I'm really excited to visit. Kyoto, with its old town, temples, geishas and if you have time a visit to the castle enroute from Hiroshima to Kyoto but you could easily spend a week in Kyoto. I've picked the Urban Hotel Kyoto as it is again centrally located and near public transport access.
30th March to 1st April
You'll return back to Tokyo for a final 2 nights at the Shinjunku New City again. You can easily move around the city or if you didn't want to stay in the same place you could choose another hotel.
You fly back to London with a short stop in Rome on 1st April.
Long haul flights book at Omega Flight Store £797.26 for 2
1 night in Rome Aurelis Art Gallery £58 @ hotels.com
2 nights in Shinjunku New City £173 @ hotels.com
2 nights Takayama Country Hotel £95 @ booking.com
1 night at Parkside Hotel Hiroshima £45 book via TripAdvisor/Raukuten
3 nights Urban Hotel Kyoto £211.79 book via TripAdvisor/hoteltravel.com
2 nights back in Tokyo £173 @ hotels.com
Book 2 x 7 day Japan Railpasses £434 @ jrpass.com