Travel in Japan with 3 years old kid

Hi there,

I wrote a blog post about this a while back, you may find it useful for inspiration:
https://www.jrpass.com/blogs/family-trip-with-the-japan-rail-pass-tokyo-kyoto-and-osaka

Now to go into your question.

1.) Yes, nearly all station do. You may find some stations with only stairs when you visit the remote country side but not anywhere in Tokyo. You can also always ask station staff for help if need be.

2.) Please have a look at the itinerary posts, I think it would match your wishes well.

3.) The travel time between Tokyo - Osaka is around 3 hours using the Shinkansen bullet trains. Kyoto is about 160 minutes/one way. You can use the Hikari bullet train directly between all these places.

Hokkaido is a bit further afield. About 4 hours to Hakodate and 7 hours to Sapporo, coming from Tokyo.

4.) Hotels are hard to recommend, we all have our own wishes and budget. That said, in Tokyo you will be fine if you book a hotel that is on any of the stations of the JR Yamanote line. This is the central loop line in Tokyo that covers nearly all the important stops in Tokyo. In Osaka, I'd stay in the Umeda area near Osaka station. It is convenient to get around from there. In Kyoto you can either stay near the station or in the center, near Kawaramachi/Shijou.

Hope this helps,
Daniel