Where is your wife from? If she's from the Kantō area, I would say its best if you are situated somewhere around Tokyo.
If she is from the Kansai area, she might be more comfortable there. Its a bit out of my area of expertise, however property prices should be cheaper in the Kansai, so your money might go a bit farther there. However, since the dialect and the vibe is different in the Kansai, your wife might find it difficult to adjust if she is not originally from there. You, as a foreigner, are immune to these regional difference since every place will be new to you, and every neighborhood will treat you the same: as a foreigner. For your wife though, the regional difference can produce real stress. So, the world may be your oyster, but for your wife, some oysters may not sit very well with her.
Anyway, for me I would want
1. Proximity to an international airport. Preferably less than two hours away. One hour or less would be fabulous.
2. Proximity to an international grocery store. Not that I need western groceries, but its nice to have a selection of wines and other things once in a while.
3. Ability to be anonymous. If you are the only foreigner around, you will constantly stand out. At the conbini, at the doctor, at the post office, at your kid's school. It was OK for a while when I was in my 20s, but it quickly became old. Now, in Tokyo, I really like being one of many tens of thousands of foreigners.
4. Two bathrooms. For a happy marriage, you ought to have two bathrooms in the house. In most Tokyo apartments, the default is one bathroom, no matter the number of bedrooms (excluding apartments made specifically for the wealthy, or expats on big salaries).
5. With kids you'll probably want to consider having a car, which means you should consider getting a place with a parking space. Not all apartments come with parking garages. Most employees in the cities do not commute by car. Companies don't provide parking spaces for employees, and many companies have rules against commuting by car (due to various insurance restrictions).
6. Conversely, if you abandon the idea of getting a car, you will want to be someplace with excellent train/subway access.
If you are game to buy a house in a suburb of Tokyo and try your hand at renovating it, I highly, highly recommend watching Jaya Thursfield's youtube channel, "Tokyo Llama", wherein he buys a substantial Japanese farmhouse and renovates it to suit him and his wife and his two kids.
Hello! My name is Jaya, I live in southern Ibaraki, just an hour out of central Tokyo, with my wife and our twin boys. In this channel I'm documenting the pr...