I find Tokyo 10x better than SF or LA for places to hang. In SF or LA they are either all full, or you have to by stuff every 2 hours which makes me fat, plus I can't leave anything out so after a coffee or two I need to use the restroom and I lose my space because you can't leave a notebook unattended in the USA. The only exception is maybe the Workspace Cafe in SF.

In Tokyo there's co-working spaces everywhere, they are cheap (especially when you take into account free drinks). Have worked from plenty of starbucks as well, except on weekends when they're full. The one behind roppongi hills that's open till 4am has been great. The one at the corner of Meiji-dori and Omotesando on the 6th floor is huge and been great too. Just don't go on a weekend / holiday.

I'd be curious to know which cities you think are good. I traveled to a bunch of cities in Europe last year and my luck was like yours in Tokyo. I looked up places, checked them out, all were horrible. But I was only in each city for a week or less so maybe I just failed to find anything like you did in Tokyo.