1. Personal favorites would have to be either Hong Kong or Tokyo. While I like them and are equally comfortable with either, I'd have to say HK's, if only because I have a much easier time with speaking and reading the local language.
2. I recall being stunned how how large Shinjuku station and the area it encompasses. The first time, I thought it was just where I had been used to getting on and off, but slowly realized it stretched out several blocks. Even now, I marvel at its sheer size and how efficiently it runs for something that large.
3. While there are many, PDX is a pretty good choice. It's clean, comfortable, a short distance from the Gate and very scenic. I also like the HK Express, but not sure if it qualifies as getting one directly into "downtown."
Honorable mentions are London's and New York's, both which I had known quite well when I had worked in those respective cities for a period of time. But, once about 6 months passes, I tend to forget and get lost all over again. When it comes to exits, I just sort of use the force, because I've never been able to read maps, have no sense of direction and no idea how to use a compass. I must waste at least 30 minutes getting lost at every new station I get off of and any familiar ones where I haven't visited in 6 months.
I find Shanghai's the easiest to learn with my deficiencies, and have, amazingly enough, never gotten lost there. I just like the those bright Arrows pointing the way to routes and transfer trains that are idiot proof, in my view. Generally, I don't like to devote any effort to reading or critical thinking on subways, and really find those bright green arrows comforting.
Paris is pretty good, but I just prefer to take taxis or hire a private car in that city. After an unfortunate incident, I will never take public transportation in that city, ever again.