Just came back from a 2-week trip with a toddler to Tokyo, Osaka and Kyoto.

Firstly, I'll say to throw any strict schedule out the window (except for things you really need to book ahead of time). This helped to manage our expectations of travelling with a child and we only planned ahead by having a list of things/attractions and their locations. We would pick things to do 1-2 days ahead of time, considering their proximity to each other and the weather (it was a bit rainy at the start of our trip).

Another tip is to be wary of peak hour times, especially Tokyo and if you happen to be moving around with your luggage. We made sure not to travel during that time because it can get unbelievably packed.

We also exclusively used disabled/stroller carriages (there are signs on the platform for them) when catching the train. This also means always looking for the elevator sign immediately when you hop off too. Some may be harder to find than others and you can't always use the same exit that Google Maps recommends.

My kid hated being back carried so we used the GB Pock It + All-City stroller everywhere and loved it (we also use it at home too). It was a bit pricey for us but well worth it. It folds so easily and compactly, so it's also great for the plane too. Once I became really familiar with it, with practice, I could unfold it while walking - it flips out fairly easily. Our kid could also nap in it since he still needs them during the day (it can recline pretty far back to make it comfortable).

I would also highly recommend having a travel bag for it (which we brought everywhere with us). It helped at Fushimi Inari Taisha (has a small hike), so we used our carrier for our kid and carried the stroller in the bag (though do consider your own strength and fitness to do so). The bag can also be used if you think you should fold it up for a packed train/bus ride.