I have been to Japan twice and lived there for a total of 3 years.  I visited many parts of Japan.  Some of my favorite places were very old, traditional places.  I loved Kyoto and Nara, of course; they are famous.  But some smaller, lesser known places were really my favorites.  Kamakura, Nikko, Hakone, Kasama, Kashima, to name a few. Hakone for example is known for its special wood work.  Kasama is known for a special pottery.  Many of these places also have famous temples and shrines.  Of course I enjoyed the cities like Yokohama for a variety of reasons, but they are too big and too congested.  I also rode a very old steam train all the way up the mountain to Gumma. That was very exciting.  It is a wonderful place to discover if you have the time. 

As the person above said it depends what you are looking for. The big cities like Tokyo and Osaka are relatively english friendly. but the rest are not so english friendly.

My favorite city in Japan is Sapporo is kinda big has a population on 1.9 millions I think, its close to nature if you want to see that, but you still have a big city. But you definitely need some japanese to survive, it will make the trip so much more fun ^-^

It all depends what you're looking for. There's so many parts to Japan, and they're not all the same. Do you want to go to the city? or countryside? How fluent are you in Japanese? There's so many factors, and it all depends on you and what you want to do and know how to do.

Narita : ) lol.