Pros:
- Safe almost everywhere even at night and generally very clean
- Infinite amount of things to do, you'll never finish exploring new restaurants (with delicious food) and stores
- International events happen there: conferences, concerts, etc.
- Very walkable (including the metro), especially around city center
- Reasonable housing prices - high, but comparable to cities in the US
- Politeness is baked into society and unpleasant interactions with strangers are very rare
- Rest of the country is fairly accessible by train for a weekend trip, and there's plenty of beautiful nature if you get out of the city
Cons:
- Difficult language and few people speak any English
- Fairly closed society/culture, you'll always be an outsider (but there are plenty of expats)
- Toilets in restaurants often suck and public trash cans are rare
- Bureaucracy is quite bad and inaccessible if you aren't fluent in Japanese
- Work culture is bad, though being remote could make that a non-issue
Some runner ups:
- Lisbon (excellent weather, low prices)
- Copenhagen (super safe, great quality of life)
For me though, the top 3 criteria by far are 1) a lot to do, 2) very safe, and 3) don't need a car, and Tokyo is pretty much the only major city that meets those.