If you unfortunately didn't have time other than year's end season (about Dec.28 to 31) / new year (Jan.1 to about 7) to trip to Japan, you should be careful not to be caught in toooooo crowded Shinkansen.
For example, if you wish to go travel by Shinkansen from Tokyo to Kyoto, you'll be forced to keep standing up for 2hour18min by Nozomi super express (the fastest Shinkansen) and 2hour 36min by Hikari express (the second fastest Shinkansen).
Why this happens?
In Japan, new year is more popular celebration than Christmas.
So tons of people go back to their home town to celebrate new year with their father/mother/grand father/grand mother.
For now Japanese population is concentrated to big city, transportation from big city to rural area will be crowded at year's end.
As you know, Tokyo is the most big city in Japan, so period from Tokyo and prefecture nearby to west Japan (Nagoya, Kyoto, Osaka, Kobe and so on) will be most crowded.
So if you are going west-bound at the season, you better reserve seats AS SOON AS POSSIBLE from JR East online ticketing site.
If it's week before you are riding on Shinkansen, there might be no more seats available.
I'll exclaim again. RESERVE SEATS AS SOON AS POSSIBLE!!!
But if you are too late to reserve seats, it's not yet the time to give up.
There's a way. Not like a magic, though. But it is limited to Tokyo or Shin-Osaka.
Why Tokyo or Shin-Osaka? Because all Shinkansen depart from Tokyo and some from Shin-Osaka.
Nozomi super express has 3 non-reservation cars (from 1 to 3) and Hikari express has 5 non-reservation cars (from 1 to 5).
So if you want to ride on Nozomi/Hikari, go to Tokyo station abour 30-60min. before the Shinkansen(which you want to ride on )'s departing time and get in order.
This might seems crazy, but it's the reality in Tokyo at year's end season(at least in 2016).
So when you arrived at Tokyo station, buy a ticket for non-reservation ticket and go through the electronic gate, and before/after the gate, check the departing time and platform number you would focus on at the electronic bulltin board.
As the same, new year season (Jan. 1-7), inbound Shinkansen train will be crowded for the same reason.
Of course if you do like to experience craziest crowded Shinkansen to get a topic to tell your friends/family, please try to ride on Shinkansen without any preparation at year's end / new year season!
Hope you'll be prepared and have pleasant trip to Japan!!