The topic moved toward Kyoto. I would just say that Kyoto is not the best city in Japan for kids, unless I am drastically missing something. Is manga, etc what interests them? I don't claim expertise in that age group for Japan, but Tokyo must be a much richer environment for that.
To each his own. You'd have to give more info about how long you are there, how rushed, etc. how old the kids are, whether you're terrified the kids will wander away in a train station, etc
We have visited Japan too many times to count. Outside of Kyoto and Tokyo, renting a car makes sense. ... maybe. Summer 2022, we spent a month in Kyoto. We did not rent a car. We used a taxi 3x. We used buses and trains the rest of the time. I can admit to being nervous the 1st morning I did it, all alone. But, the iPhone's directions app is awesome. It handled Kyoto like child's play. In a month, I got lost once. A bus I was on turned south when I wasn't paying attention, but I figured it out within 2 blocks. I pulled the cord, told the bus driver what happened and that I meant to go west. He gave me a bus pass, pointed at the bus stop across the street and told me which # bus to take.
Kyoto is a N-S, E-W grid. Just keep focused on an imaginary compass (or heck, bring a compass). On the trains, you have to get used to counting stops, which you mostly have to do in Tokyo subway anyways. And in Kyoto, having a car means you have to find parking at the major tourist sites.
I do not recommend a car in either Tokyo nor Kyoto, but we love to walk and are not afraid of Japanese words presented in romanji.
Of course, if you have a group of 4 or 5, it leans toward using a car.
