If you have any of the following go green:

Lots of luggage, travel during a holiday, or really want a big seat with a leg rest.

However, if luggage is the issue, don't forget you can drop it off at your hotel concierge and have it delivered to your next destination (usually next day). I did that for a Tokyo to Kyoto trip, worked really well, and it was nice not to have much to haul around at the train station.

No matter what, I'd suggest reserving your seats right away. When you convert your Exchange Order for the Rail Pass get the reserved seats right then and there.