I have been to Japan about 4 times within the last 2 years (each trip about 16 days) and must say the transportation and service level is outstanding. However be aware you may have problems communicating easily if you don't speak japanese. I had to arm myself with some useful phrases from the guidebooks and relied on "sign" language - however quite a few of the tourist sites can give brief advice if you make your enquiries easy for them to understand in english.
We went in May, October, early Nov when the weather was cool. I am not sure when you are travelling. This year's winter is really harsh so I am not sure what it's like to travel to the places we are recommending during winter.. We made sure we stayed MINIMUM 2 nights at each place.
Here are some very useful websites:
For transportation, besides jorudan link which was given earlier by zags, here'also the JR website
It gives you the fastest way from one destination to another for JR trains which is one of the largest rail network in japan. If you also click on the icons under "timetable" (book icon) or "Info" icon, it opens up to the various schedules available and how many stops between the stations.
When travelling in japan by rail, you must be very sure of your routes because it can be terribly mind boggling. I usually cut and paste the schedules on Microsoft Word and print them out. Since I don't understand japanese, I even make sure I know how many stations and the names of the stations between my departing station and arrival station. This will save you lots of headache becuase their train stations have so many trains departing from several platforms.
As for the japan rail pass - it's best you do your homework using the transport link we gave you so you can calculate if it's worth it. The good part about the pass is you can make reservations without paying extra for these seats. I only used the Japan Rail Pass on one of the trips because I was staying for a few nights at a place and unfortunately the Pass is for consecutive days so in the end it worked out cheaper without the Pass.
One piece of advice - make sure you get on the right train because trains leave within minutes of each other. If you arrive early and you see the train - don't assume that's the one. Check the platform sign before you board.
Also the subway lines are different - try to get a map of the subways from the Information desks which are sometimes located in the main cities like Shinjuku, Tokyo etc. Or you can download from the Net.
By the way, there isn't enough room on the trains to put your huge suitcases (except narita express from the airport). Although the leg space is wider than those in the airplanes, you wont be able to place these large bags in front of you or on the overhead - it's best to use one of the cities as a base and then use a handcarry for the side trips. If the bag is small enough to put under the airplane seat, it should be ok for you to take it on the trains.
Erm...NEVER NEVER TAKE THE TAXI - IT COSTS AN ARM AND A LEG. The train network is superb and if you choose the right accomodation, you can use your legs which is cheaper.
Most of the places in Japan are famous for the shrines or temples eg. Nikko, Kamakura. However for those who aren't so keen on visiting these places (like us), there are still other interesting places to see:
If you enjoy japanese food like sashimi,and those wonderful dishes that are painstakingly prepared (we absolutely loved it) etc. you must must try one ryokan experience at least.
I don't think one has really experienced Japan if you don't stay in at least one of their ryokans. It's crazy but from all the visits, we must have tried at least 5 ryokans and their hotsprings - wonderful although it made a dent in our pockets (worth it though).
Here's the link to JapaneseGuesthouse which is an excellent service for tourists who need to look for a nice ryokan. But avoid enquiring if you aren't sure because they are really serious about their work and it isn't nice if we waste their time by getting them to call up so many ryokans if you aren't really interested.
Look for the ryokans which has outdoor hotsprings and go for the experience. It's like no other and you will never be able to experience this outside of japan. They may seem to cost abit more than usual because they charge by person eg. $270 per person a night. But when you look at the amazing traditional kaiseki dinners (with many dishes) and the breakfast, it's value for money. Asians by and large wont have problems with these kaiseki dinners. Westerners can request through JapaneseGuestHouse about any food preferences. Best to skip lunch because dinner at these places are served between 6-7pm and believe me the dishes seem never ending.
However if you are travelling alone, I am not sure if japaneseguesthouse will do bookings for singles. You may have to go directly to the ryokan website to ask (unfortunately many websites are in japanese).
Fuji5LakesKawaguchiko is a nice place to visit - esp the Forest Box Museum, the Kubota Art Museum with fantastic landscape kimonos. There's also another Art Museum with lovely large photos of Mt Fuji with different cloud formations, lighting, seasons etc.
Allow yourself about 2 nights in Fuji5Lakes. One night is a little short because there are certain "shows" at the Forest Box Museum at different times of the day and you don't want to have to rush around esp so if the weather may be bad on that day.
Stay around Lake Kawaguchiko where access to the tourist sites are easy on the Retro Bus. If you are fortunate, Mt Fuji is spectacular on a clear day. We saw her in her fullness one of the mornings outside our ryokan balcony, totally unblocked by clouds.
We stayed at Hotel Konanso, a japanese ryokan which is a very convenient spot for sightseeing. We booked this under Japanese Guesthouse.
We also stayed at Hotel Petite Mermaid which is at the last stop of the retro bus (7mins walk). This is the only western little chateau hotel with a quaint french restaurant with Mt Fuji view on a clear day. Decor is pretty english in style with wallpaper. We found it refreshing to have french dinners after so many nights of japanese food.
Oh if you are one for rollercoasters, you must go to FUJIKYU HIGHLAND which has one of the best rides in japan. Mt Fuji is in the background. There's another ride which shoots you off at top speed. These 2 rides beat any from Disneyland tokyo. This themepark is one think just one train station away from Fuji5Lakes. There is even a Fujikyu Highland hotel there.
The following link has some info on Fuji5Lakes and is also a useful link for getting to other parts of japan.
In Tokyo, the Tokyo Edo Museum is definitely worth seeing. The train station is RYOGOKU. I am not one for museums but this was really interesting. If you go to Ryogoku, that's where the sumo staduim is - go to the restaurants which serve Sumo Stew called CHANKO NABE.
There's so much to share and I can't cover everything on this page. Just bear in mind the type of weather you will encounter. Eg, we visited Kamikochi valley which is so beautiful, using Matsumoto as our base. Also the Kurobe Alpine route but these places are extremely cold in winter (Dec-feb) and probably heavy snowfall.
I had to do a lot of homework on the Net and bought 5 guidebooks to do my research and it paid off because we had a fantastic time travelling free and easy (but booked accomodations in advance).
Go to google search and type in whatever you are looking for.
If you want no frills very clean accomodation, toyoko inns are very useful. Safe, clean although a little small but great for those on a budget. You can check out this site.
In Shinjuku, StarHotel is also a clean business budget hotel which is easy walking distance to the JR station.
We are from Singapore and our experiences are based on personal preferences. Everyone has their own set of ideas and tastes - ultimately you need to do your homework through the Net and guidebooks depending on what you are looking for.
We loved the natural landscape and scenery although I must say the architecture is no where as artistic as that of Europe. I think we enjoyed travelling in japan because people are polite and it's just a joy shopping or eating there.
However, buildings in japan are pretty much like concrete blocks esp in the cities but I must say the neon lights at night + all those vending machines make their cities pretty unique.
So if you are really looking for a unique experience of Japan which you can't get anywhere else in the world - I would have to say it's the ryokan experience. If you can, try to get one where they serve the dinner in your room.
Japan is a very safe place and people are courteous and respectful of each other. Only the language barrier may post a bit of a problem but it shouldn't keep you from enjoying yourself.
All the best!