I worked in Tokyo for a while. If you don't take cabs, you end up doing a fair amount of walking. There are a lot of trains and subways, so there is a limit to how much walking you have to do. Even if your origin and destination were both right next to a subway station, however, you could expect to do a lot of walking underground, since there is a lot of stuff underground in Tokyo around which subways have to be routed.
I think walking is great, and frequently I would figure ways to skip a subway line by walking a bit more, but I thought I'd mention this just to give a more accurate impression.
Berlin has a fantastic transit system. I was living almost in Potsdam, and I could get to Mitte in under an hour - and the trains and buses were almost always on the dot on schedule. Before I lived there for a few months, I had only really experienced the Boston T system, which is seemingly about as bad as a transit system can be and still be considered functional...