Most people build a new house because that's the dream: to live in exactly the house you want to live in. If you buy an old house, then you are putting up with somebody else's choices. That and the fact that until recently houses weren't built to last. You seriously don't want to live in a house built in the 1950's. It wouldn't even take an earthquake for it to fall down around you and kill you ;-)
Housing standards have improved dramatically over time and the difference between at 10 year old house and a new house was historically stark (well, at least since WWII). These days it's starting to even out and I see the used house market starting to pick up a bit (personally, I even prefer the houses built 10 years ago to the ones they build now -- It seems nobody wants windows in their new houses any more...)
My sources say that this is a long held artifact of the shinto belief system and culture. This is a clumsy way to state this but they essentially that houses accumulate spirits over time and become “haunted”. Old dwellings are valued less because they are “dirtied” or “burdened” with an accumulated cruft of spiritual... somethingness. Haunting here isn’t a literal translation but it’s the best I can do in a short time. It’s kind of how Marie Kondos whole schitck is about treating your things as if they have “personness” or “the quality and dignity of being actively present and deserving of respect”.