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A stroller will force you into taking long convoluted paths on public transport, in shopping centres and large stores. Unlike in other countries, strollers are discouraged and often prohibited on escalators unless they are folded up.
There is a strong and pervasive baby carrying culture in Japan.
The downside is using taxis without a baby car seat.
But that's a problem shared by other Japanese families. If you ever spend time at Tokyo station queuing for a taxi you'll find other families with infants strapped to them waiting for their rides also.
On trains, if carrying your baby, be sure to aim for the dedicated priority seats for the disabled, elderly, pregnant and child porters. Occupants of the non dedicated seats will not be nearly as ready to offer respite. If you look carefully at the floor signs on the station platform you will start to see the clues showing where to enter the trains. Even so, the journeys are (generally) far less jolty than journeys elsewhere. Many parents with kids strapped to them seem to prefer to stand.

My experience was very different to evergreens. At 6 months my kid was fine strapped to me for very long extended periods. She napped on me beatifully. Lots of baby feeding areas in commercial areas and large stores, I appreciate not everybody is as comfortable walking around breast feeding (with a modesty blanket) as I was.