Suzanne said she heard from a friend that had visited Japan that the public transportation was one of the trickier aspects of the country so she suggested watching youtube videos and tutorials. That was an excellent idea. We also purchased an all-access train pass. The trains covered all our travel between cities and a lot of our travel within the major cities. But we also had to learn the subway systems and the city bus systems. We found that we had about a 24 hours learning curve and we were in each city for about 48 hours so we'd learn the system, enjoy our vast knowledge for a day, then move on to the next city and repeat.
Before we even got to try out the subways and trains, we flew into Tokyo late in the evening and had an early flight out the next morning to fly to the northern island of Hokkaido. We booked a hotel room near the airport and got in a cab. We asked him to take us to the Royal Inn Hotel Haneda (Haneda is the name of the Airport too). He took a minute to figure out where this hotel was. We figured if he was driving at the airport, he would know the hotels in the neighborhood, right? Surely this wasn't more than 5 minutes away. He asked if it was a new hotel? Then he laughed and said "this is IN the airport!" Then he started driving while laughing. Then we thought, wait, if this is IN the airport, where is he driving us? He is just going to drive us to the other end of the terminal, to the door of the hotel. He wasn't really familiar with it, but knew it was at the end of the terminal. He drove us down to the end, no entrance. He drove us the other side, no entrance to the hotel. He drove us around the airport terminal for 5 minutes or so then drove us back to the EXACT SAME CURB where we got in and finally figured out that if we walk back into the terminal, go up the escalator, turn left and walk 100 yards or so we would be there. Then he charged us $13 for our ride. Yes, a ride to the exact same pickup location. I asked Dave later why didn't he argue the fare. He was literally so exhausted and didn't even have the words in Japanese to argue - easier to just pay and get to the hotel on foot!
Transportation on the first day in Hokkaido was a bit traumatic. The first resort we stayed in the first day in Sapporo assured us they had a shuttle - which somehow did not pan out for us so we took a city bus way out of town. The trains and subways had a lot of instructions and helps, but the city buses did not. We hopped on the bus hoping it was the correct one, could not understand the announcements, weren't sure what time we would expect to arrive at our stop, weren't sure we could hear the announcement for our stop, the bus was SUPER crowded, and we had a little bit of a panic attack and we realized if we missed our stop (which was supposedly a 2 minute walk from our hotel) and the sun was going down, and it was getting colder and colder and we were farther and farther from the city center (access to taxis) and we were hauling our luggage, we weren't sure what our Plan B was, and if we went past our stop we weren't sure how to get back. As it ended up, (all while we were in a panic) more and more people were getting off the bus, it was getting emptier and emptier (thus enforcing the idea that we probably missed our stop) then the bus came to a stop right in the parking lot of our resort, the end of the line for the bus driver for the day! Yay. It also made it easier to get back on the next morning knowing we'd be the first ones on and were assured an actual seat.
The other crazy transportation situation was a day we tried to do maybe too much. We were staying in Kyoto and decided to do two out of town things in the same day. We left our hotel at 6 am and took the "Shinkansen" bullet train to Hiroshima. We spent about a half day there and then wanted to also visit an island called Naoshima. To get to Naoshima from the bullet train required us to transfer to a local train, hop on a ferry, then take a local city bus across 20 minutes or so across the island to where we wanted to go. In order to do this all in one day, we had to make sure we were on the last ferry off the island so we could be on all the connections to get back to the last bullet train of the day. If we missed the bullet train, we would be on a local train and would turn a 90 minute trip into a 3 1/2 hour trip back to our hotel. We were also expecting a call from Melanie as she was leaving the MTC that morning (our night, her morning) and needed to be back at our hotel to get her call. Naoshima was one of our favorite places so we were glad we made the effort to go, but we were worried about making all the right connections to get back to Kyoto by the end of the day. We were on the far side of the island with quite a walk to the bus station. At one of the museums, there was a chartered shuttle bus for the local resort peoples. It was heading the in the direction we needed to go so Dave and I jumped on and we just sat down and took a ride back to the resort, hoping no one would ask for a ticket or verification that we were staying at the resort. We made it to the bus stop, made it on the ferry, ate dinner at the 7-11 as we were walking to the train station (they sell egg salad sandwiches everywhere), made it to the local train connection, then when we were running for the connection to the bullet train, Dave heard it coming in (and they only stop and open the doors for exactly 60 seconds - I timed it - and close the doors and take off). We were running for it and rounded the last corner and looked up at THREE FLIGHTS OF STAIRS! Oh my heck we did a lot of stairs in and out of the subways this week! We made it to the top as the buzzers were going off for the doors to close. We dived in the closest door and they shut. I was asking Dave if we were actually on the right train. "I think so". But since we jumped in the closest door, we had to hike through 12 cars on the train to get to our assigned seats. Then we anxiously waited for the digital board to show the next stop to verify that we were actually on the correct train barreling down the tracks at 150 miles an hour.
All in all we utilized - planes, trains, automobiles, monorails, taxis, trams, buses, subways, cable cars, escalators, elevators, and our poor tired feet. I think we used everything but bicycles and a rickshaw.