It had everything, insanely good transport, safe, some of the best food in the world, beautiful weather most of the year except for rainy season, incredible art, great mix of old and new, some beautiful parks, great for riding bikes, little traffic, clean air.
The only thing I’d say let’s it down and it does let it down a bit is the lack of greenery. I think it’s a known issue though.
It’s honestly the best city I’ve ever visited and I’ve been to a few.
New York is a close second for the history but it’s so dirty that it’s beyond charming.
From a european standpoint it makes it really hard to live.
As for cycling, I can’t speak to it as much, but it seems like the cycling culture is much more casual. Tons of parents cycling their preschool children, people biking on sidewalks, etc.
That said, my best mate is an avid cyclist and worked bike shops most his life. He exclusively cycles here and always points out the sheer number of hobby (expensive? custom?) bikes casually posted outside shops.
Also, there are plenty of terraces to have a nice coffee on. The difficult thing in Tokyo is you need to search in advance for what you want. It's so crammed full of options, that you might never realize all the interesting things you're walking past. It's a very three-dimensional city, there's stuff hidden everywhere.
I would say a few downsides are poor insulation from noise and weather in many buildings and expectation that children don't make much noise (it is really sad to see signs in small parks that say "no ball games"). I also echo bsaul's comment about the lack of terrace space for restaurants and cafes, those are great public socializing spaces.