One key difference that jumps out at me between various cities in Japan and Vancouver is that the COL seems significantly better in Japan. When I visited Vancouver I couldn't afford to stay in or even near the city, I had to find a place about 20 minutes away and even then it was pricey. Whereas in Japan I had no problem finding affordable stays in city centers in all of the major cities I visited, including Tokyo.
I will admit my ignorance here however and acknowledge there are likely myriad other variables at play here that I'm not considering.
Affordable to you or affordable to the locals? The yen has devalued a lot in the past decade or so, giving foreigners a lot more spending power in Japan and causing the current tourism boom and backlash.
Still affordable to locals. The yen has devalued, and the cost of mansions (condos) have gone up, but single family homes, small apartments, etc are still similarly priced to buy, and rent is generally stable. A major difference is that if you are OK with a tiny apartment, you can get one, and it'll be something you can pay.
You can definitely see affects of the poor economy lately (lots of pawn shops popping up, replacing expensive cafes/restaurants), but housing is still reasonable for now.
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As a visitor, it's probably impossible to know the real cost of living is in different areas, because you're not employed locally, paid local wages, or paying rent and utilities. You are a foreigner with foreign money staying in hotels.