Tokyo's fees are not so expensive for public transportation if you have ever been to other cities in Japan. In fact, it is probably the city where you travel a very long distance with a reasonnable fee, something like 1.5 dollar or so. In other Japan cities for the same distance, the fee can double or triple, so Tokyo is rather cheap in that aspect.
The parking space problem is only solved because everyone is using the train to go to work everyday, mostly. If this were to change, they would face major parking space issues, as the innards of the city are not designed to park a great amount of car. The parking space you mentioned is usually the one you reserve in your building when you get a car, but that does not mean there is space available at your destination.
It is quite inefficient to travel in Tokyo altogether. While not too expensive, it takes a lot of time and in the train you cannot seat most of the time because it is overcrowded. I would not pick Tokyo as an example of a city where things work well - it just works, but it's already over-capacity.