My understanding (albeit only gathered from blogs/YouTube videos/Google Maps) is that the biggest difference is parking. On-street parking is mostly not allowed, free parking at businesses is mostly limited to car-centric ones like mechanics and dealerships, and you can't register a car without proving that you have a place to park it. Tens of millions of Japanese people living in less-dense areas have no problem with that, but in Tokyo it's prohibitively expensive for the average person due to land cost. This means that even in suburban areas, roads are narrower and everything is closer together.
When I worked in Japan for a year and lived in the company subsidized dormitory, a coworker half-joked that it cost more to house his car in a payed parking spot than it did to house himself in the dorm.
When my grandfather passed away the deed for his Manhattan parking spot was far more valueable than the five bedroom home I grew up in.