If you only want to travel between Osaka/Kyoto and Tokyo, a cheaper option to the JR Pass is to get a Platt Kodama ticket http://www.jrtours.co.jp/kodama/en/ which is for the slower shinkansen. The only issue is that they don’t serve food on the train. We didn’t realise and we’d skipped breakfast thinking we could get something on the way!

If you have more time than money and you are in Japan at the right time, the Seishun 18 ticket is super cheap. You can travel on any local trains for 5 non consecutive days for 10,000 yen. The original intention was a cheap method of travel for uni students on holidays but anyone can use it. You can even share the ticket (eg. 5 ppl travel for 1 day or any mix of that).

I’ve used it a couple of times and while it’s slow travel you have a lot more flexibility than with the JR Pass. There are sites that show the best routes to use the ticket to get from one end of Japan to the other but I found I was limited by the amount of time my butt could handle sitting on those local trains!

Car travel for long trips isn’t really a thing in Japan even for locals. As well as the issues you mentioned, you can get stung with really hefty road tolls. It might be worthwhile for a large family but otherwise, everyone catches the train.

But one thing I really love is that you can get short term rental cars for like 6 or 12 hours. So if you’re going to small towns that don’t have good public transport options, you can catch the train then rent a car for half a day at the station, do your day trip and return the car. That also saves the hassle of needing to find accommodation that includes car parking. From memory, you do need to have an International Drivers’ Licence.

Only Tokyo has Uber and the prices are more expensive than cabs. Catch the train. It’s actually the fastest way to get around but use Google maps or Hyperdia to plan your trips.

I think it’s important to note that transportation is the most expensive part of Japan. Healthy, high-quality food, clothing, electronics and even accommodation can be quite affordable for large cities like Tokyo, Kyoto and Osaka. Most people don’t expect this.

If you are traveling in the off-season, it might be a good idea to check in with a travel agent in Japan to see if there are any last minute deals. My family got a hotel/onsen package with Shinkansen from Osaka to Kagoshima for less than the cost of the train tickets. Basically, the hotel and buffet breakfasts were free. Golden Week (April/May) and Obon (August) are crazy expensive, but there are good deals to be found outside of those dates.