When To Buy Jr Pass -
You want the Narita Express or Haruka (Osaka/Kyoto) included in your travel days. When to Skip It (Buy Single Tickets Instead)
The fastest bullet trains require an extra "supplemental" fee even with the pass; individual tickets let you book these directly. Pro-Tips for Timing when to buy jr pass
To help you figure out if it's worth it for your trip, tell me: What is your ? Which other cities are on your "must-see" list? How many total days will you be traveling? You want the Narita Express or Haruka (Osaka/Kyoto)
Buying from the official JR site allows you to book seats online for free before you even arrive in Japan. Which other cities are on your "must-see" list
If you are only exploring one area (like just Kyushu or just Hokkaido), a Regional JR Pass is much cheaper and more effective.