Two things I will call out as actual disadvantages is that 1. you won't be able to get a mortgage like a normal Japanese person, which is in fact a real shame because on top of every other ludicrously wild fact about how Japan is a mythical utopia where everything makes no sense, Japanese mortgage rates are literally as low as 1% lol. So being able to get a mortgage would be a real benefit, but hey - at $60k for an awesome house, I'm not complaining :)
2. Some insurers seem to not support foreign citizens - Sony in particular told Dot that they wouldn't provide earthquake/fire/flood insurance to me as a foreigner. I'm still looking for the right insurance provider, and I'm not concerned that this is an impossible thing to resolve, since a ton of foreigners do own homes here with no issues, but it is at least some more friction than a Japanese citizen would have.
Most regular people can only visit Japan for 3 months out of the year. Even if you buy a home you can't get a visa just for that.
Maybe in your case the visa thing isn't an issue because of your wife but that won't be the case for most people.