If I want to visit Japan for two weeks with wife and toddler…

1) Best month to visit to balance good weather and cost?

2) Best 2 cities to stay that are family friendly?

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The fall is ideal!
Every major city in Japan is pretty family friendly in Japan, so wouldn't be too concerned on that front!

Tokyo will have the most to do, but hotels are pretty pricy.

If you're looking for something a bit more off the beaten path Hakata and Sapporo could be fun!

Kyoto is the biggest tourist destination if you're interested in seeing more of the historical center of Japan as well, with easy access to the rest of the Kansai region (Osaka, Kobe, etc.).