There a four phases of cultural adaptation, and I'm pretty sure I'm still in the first, enchantment. I think that Tokyo is the greatest place I've ever lived. Sure it's crowded, huge, and massively busy, but there are little stores and shops everywhere. If you need to go to a shopping center, there is one in every direction only 15 minutes away by train. You can get everywhere by train. Things that are not at a station are generally only 10 or so minutes walk from the nearest one. We across the road from one subway stop, and about 7 or 8 minutes walk from a good size transportation hub with 4 subway lines and a JR line. It's about 10 minutes on any of those to one of the massive trains stations that have 10 or so lines.

It's hard to compare Tokyo to other large cities, because I've only visited a few.

LA - no comparison. If they had public transit everywhere, it might be as livable. But as long as you don't have to go more than a couple miles there, it's a nice place to live.
DC - Again, a lot like LA, only with less roads and worse traffic.
Atlanta - Roads, no transit. Pain to get around.
London - I think London is a lot like Tokyo. Completely different culture, but from a livablity standpoint, I think it works.
Chicago - Seems easy to get into as long as you are on one of the main transportation cooridors, and it has a lot of great neighborhoods.
Hamburg - Great transit. Nice neighborhoods. etc.
Vienna - Ditto
Rome - Ditto