In spring season, the busiest period is late April and the beginning of May. It is called “Golden Week” in Japan. April 29, May 3, 4, and 5 are National holidays. If you can, lease try to avoid travelling on those days.
Some part of winter season is the busiest period. Especially in Japan, New Years holidays are crazy busy. In this year, December 30, 11 (Fri) and January 4, 12 (Sun) will be busiest days. Please try to avoid taking a train on those days. the vehicle occupancy rate may be more than 200%. Sometimes it is almost impossible to get in or out from the train.
Even though Japan is very small country, Japan have several climate zone. It is icy freeeeeezing weather in Hokkaido. South part of Kyushu have very mild weather. It is very interesting season to travel. But if you travel in Hokkaido, Tohoku or Hokuriku region, please expect the delay due to snow. I do not recommend you to make a tight schedule.
This itinerary includes many popular spots throughout Japan in 14 days. This itinerary starts from Tokyo. But if you want to start from Osaka, you can start from Day 11 to Day 14, and then start from Day 1 to Day10. Actually 14 days in not enough to see all popular spots in Japan. I include Hokkaido in this itinerary. But it does not include Shiretoko because of not enough time. I could not include south part of Kyushu, Hakone and Mt. Fuji either. If you can give up Tohoku part, you can get more time in Hokkaido. Of course you can go to Shiretoko.
Kushiro Shitsugen (Kushiro marsh) is national park and has the largest marsh wetland in Japan. It is well known as the home of endangered Japanese Cranes. JR Hokkaido’s Senmo line goes through this wetland and gives you a great scenery. Kushiro Shitsugen Norokko train is operated on this line from late April to late September. This is the easiest way to enjoy a day excursion in Kushiro Shitsugen from Kushiro. And Kushiro can be reached by Limited Express Super Ozora from Sapporo easily. Both Super Ozora and Kushiro Shitsugen Norokko train are fully covered by Japan Rail Pass.