Japan Public transportation - what didn't we conquer

Alivia and I have traveled on every transportation system (subway, shinkansen -fastest trains in the world - trace knows them from his train books- bus, tram and walking, lots of walking) in Japan except a rickshaw and what they call the rope ride which are the pulleys that take you up mountains - which i guess we will have to do next time. (there is one in Kakone, but it was fogged in so not worth it so didn't see mt fuji.) What we have learned and traveled on.

1) get a Japan Rail pass. You have to get one outside the country. Completely worth if you plan on leaving Tokyo. Can use inside tokyo and travel anywhere in the country. Saved me hundreds of dollars. Also used it on the ferry in miyajima, ended up there by accident but was well worth it.
2) you can get reserved seats (if you book through JR offices) do not spend the extra money to upgrade. You can also hope on any train non-reserved, but you may not know which ones are express so we tried to get ours through the offices.
3) get day passes, wherever you go. You will save money even if you don't think you will use much transportation. Would have saved a lot in Tokyo in the first few days if had used them. lesson learned.
4) Never get on the Nazomi - it doesn't take the JR pass.
5) skip taxis they are expensive, you can get anywhere with their mass transportation system.


Tokyo - subway and JR trains. There are three different, major train lines in tokyo. You can't go in between them on one pass. We had JR pass for 7 days so did not activate until i knew we would be doing our major traveling. next time will get day pass in tokyo for subway. you can get anywhere on that. If it doesn't take your day pass, it isn't the subway. that is how you will know. Get a map for all the trains, it is best if they are layered on each other. Once you activate your JR pass, you can pretty much get anywhere so don't have to use the subway again. Big money saver.
Kyoto - bus is best, subway is limited. Buses are set-up for tourists so very easy. can't use JR pass.
Hiroshima - use only tram (#2). Can go anywhere in Hiroshima on 150 yen. don't get on the bus. Very few people speak english, it is for the locals and much more costly. Can also use JR line but will miss the memorial peace park which is worth seeing. Get back on tram to go to miyajima which I highly recommend. Can use JR pass for ferry, then get on JR train. (You will pretty much have seen hiroshima now) will take you pack to the major station)
Hakone JR train to bus to pirate ferry (not kidding). Beautiful country but eerie as was fogged in.
Nikko - JR train, loved it the place.
Kamakura - JR train