It's easy if you use a fare/route finder like
Welcome to Jorudan Co.,Ltd.. Without this, even if you are Japanese, taking a new route without planning ahead is a bit difficult. I think getting around Tokyo is actually a lot easier than outside of Tokyo. Out in the countryside you don't exactly have huge maps posted in English in the stations like many do in Tokyo. Overall though I would say that some people are born to travel and have a natural ability to find there way whereas some are just completely hopeless no matter the tools available.