Originally Posted by jib71

I think you'll probably need to scale back expectations with the itinerary - The three days starting with Day trip to Nikko (4+ hours round trip and high intensity day if you want to see more than a couple of sights), Night around Mt. Fuji (2+ hours travel and a change of hotels), Travel to Kyoto (2.5+ hours travel and a change of hotels) seems like a lot of movement and disruption. Your jet-lagged two-year old might not handle this very well. I don't know your two-year old but the two-year olds that I do know would be altogether more amenable to a slower pace - so perhaps you could keep the same list of places to visit but stretch things out..

Originally Posted by LapLap

When is this itinerary for? Winter, Summer, Spring?

With a 2.5year old I agree about a “slower” pace, not to make the visit actually slower but to ensure play time, play time and more play time.

My number one recommendation when visiting with a kid that age is Akebono Kodomo No Mori on the outskirts of Tokyo. Free to enter. Pick up your own picnic lunch en route as food isn’t sold there. Leave the Ghibli Museum for when the kid is older.
Other toddler highlights are:
The Nihon Minka En (just having the space to play peacefully with sticks and stones and discover nooks and corners in this environment is magical.)
Showa Kinen Koen - a Park as fabulous for adults as it is for children
The Benzaiten cave shrine in Hase Dera Temple (as an adult, you’ll need a good strong back for this, the ceiling is extremely low)

Both children and adults’ expectations for these children differ as wildly as with anything else. My own was exceptionally active and, let’s say, “unpassive”. She rarely slept during the day. Her surprising appetite for good sushi at 2 and a half (her Japanese grandfather was doting and generous in this regard) is still remembered as family legend and chuckled about, to this day she remains hugely fond of ikura-salmon eggs.

Originally Posted by LapLap

Wanted to share a treasured highlight from when LapGirl was 2.5. It was at the Tokyo Edo Open Air Architectural Museum. LapToddler boarded a Tram and made a friend there. The driver controls became a cafe kitchen churning out dango and ichigo daifuku for their grateful customers. They played together for about an hour and it could have been anywhere, but what really made it possible was time, not being in a rush.