The Japan Rail Pass could be a great deal if you plan to be doing a lot of train travel during your stay. However you must be familiar with its rules before deciding to purchase or otherwise you will end up paying more and wasting precious time.
Rule 1: It's not good on the Tokyo subways/any private line
If you plan to stay in Tokyo for most of your stay, you will be using the subways a lot more, which is not covered in the Japan Rail Pass
Rule 2: You cannot use it on the Nozomi trains
The Nozomi series that runs along the main route serving Tokyo-Kyoto-Osaka-Hakata cannot be used with the rail pass. These are the most frequent and fastest trains, so if your time in Japan is limited, it might be better to buy tickets as you go.
Rule 3: You need to go to a certain location for exchanging your voucher
Activating your Japan Rail Pass requires showing the passport, filling out certain personal details and receiving explanation about its rules. It's only done at designated stations so you need to know the location. During the peak travel season, the activation could take up to two hours of waiting, if you decide to do this at the airport or at a major rail station like Tokyo. Again, this will be a major waste of time if you are going to be on a tight schedule.
Price comparison : Rail Pass vs. Buying tickets as you go
The one-way fare for a reserved seat on the Shinkansen
Tokyo - Kyoto: 13,910 Yen
Tokyo - ShinOsaka: 14,450 Yen
Tokyo - Kanazawa: 14,120 Yen
Tokyo - Hiroshima: 19,080 Yen
Tokyo - Shin Hakodate Hokuto (northernmost stop): 22,690 Yen
Tokyo - Kagoshima Chuo (southernmost station): 30,280 Yen
Meanwhile, a 7 Day Rail Pass costs 29,110 Yen, a 14 Day Pass costs 46,390 Yen...
If your itinerary calls for you to fly in from Tokyo and out from Osaka (or vice-versa) , i.e. you are only doing one-way between Tokyo and Osaka you should not bother to purchase the rail pass.
It's hard to make a call for doing a simple round-trip between Tokyo and Osaka, but if you have plans to use the Narita Express Train (3,020 Yen), you'll end up saving a few thousand yen with the use of the 7 Day Rail Pass.
Green Car (1st Class) or Ordinary?
Another option to consider is whether to go for ordinary cars or the Green Car (1st Class).
On the ordinary cars, the seats look like this photo- a 3 + 2 format. There is plenty of legroom, and for an average sized person this gives enough width. The green cars come in a 2 + 2 seating arrangement, so you definitely get more elbow room and slightly more legroom.
There is no drink/meal service or departure lounges like some European train operators offer to first class passengers. The only difference is in the seat arrangements. You'll be paying about 50% more for the Green Car seats.
A question to ask yourself- are your plans fixed or do you plan to decide as you go? Riding the Green Car means you always have to get a seat assignment BEFORE you board - always going to the ticket office even when there are long queues and getting the seat designation. You cannot simply hop on board and find some empty seats if you are using first class. This might become a bit of a hassle if you want to leave your plans flexible and decide at the last minute on which trains to take.
On the other hand, if you are travelling in the peak season, you may want to make the extra investment for Green Car. Even when ordinary class seats sell out, there is a chance Green Car seats will be available as they rarely sell out.
The below period is when trains get exceptionally busy.
The "Golden Week" Holiday period - April 27 - May 6
The "Obon" summer holiday period - August 10 - August 19
The Year-End/New Year period - December 28 - January 6
In the first half of the peak travel times, trains heading out of Tokyo becomes packed; the opposite occurs towards the end when trains returning to Tokyo becomes crowded.