Transportation in Tokyo

So we all know the trains are infamous for being over crowded in Japan. We may even think of the trains as expensive. But for the most part the trains are only crowded during rush hour and not very expensive. I didn't buy the JR pass against the advice of many travel guides and online blogs. I have about 4 days left in Tokyo and have only spent 8,000 yen with money still on my card to last the final days on transportation. This is roughly $90-$100 depending on the exchange. The 14 day JR pass was about $400 so it was cheaper for me to just pay like the locals do.
Now, if I had to pay for the trip to Nikko or Fujiyama it would have definitely been cheaper to buy the JR pass by a lot. A trip to Fujiyama would have cost about $250 on top of what I spent in Tokyo. But my advice to those who are staying in Tokyo and don't plan on leaving the city at all is to just buy the Suica card and fill it with money. Suica cards can also be used to buy locker space and at most convenience stores.

As for crowding on the train, I can say as an American I can't stand it. Just when you think no one else can fit 5 more squeeze in. It's hot, stuffy and invasive. If you can avoid taking the trains early in the morning and after 6 I would. It has been my least favorite experience of Japan by far.

Taking a taxi is very expensive in Tokyo. Do NOT miss the last train or wait for the first train at 4:30 am. It can easily cost $200 on a trip that would have cost about $10 by train.

Driving in Tokyo can be faster than the train or it can be two hours slower depending on construction and traffic. Unless you have a Japanese license or International license. Honestly the train is truly the best way to go about Tokyo.