Regarding large suitcases (the mention of which always seems to draw negative reactions and in most cases the stock reply that you should use the luggage forwarding service known as takuhaibin, even though in my experience that is not all it is cracked up to be), I have found that two smaller pieces of luggage, stacked, are actually easier to deal with, especially on trains. On my last trip I used a cabin-size small suitcase plus a rolling briefcase that could stack on top of the suitcase. I did use takuhaibin strategically to dispatch the small suitcase, and then the rolling briefcase was just great (I had a fold-up tote bag that could stack on top of that). The small suitcase (which had an expansion joint although I didnft always use it) plus the rolling briefcase together held almost as much stuff as a larger suitcase would, but the briefcase actually held all I needed for short segments of the trip. I additionally had a daypack-sized backpack that I never had to stuff very full. I am not a light packer myself, although over the years I have learned to get by with less and less.
Ifm not telling you to use this exact configuration of pieces (on an earlier trip I used a small suitcase plus a medium-sized expandable duffel bag instead of a rolling briefcase) but to consider the possibility that two pieces can actually be easier to manage than one. (And you wonft have to reserve space on the shinkansen.) I really donft know why so many tourists insist on bringing one large (often huge) suitcase. Dividing things up into two smaller stackable pieces makes it much easier to use the top shelf on the shinkansen (and some limited express trains), and when stacked makes for a smaller gfootprinth if you are on public transit. At my age and strength, I could not lift a fully loaded medium or large suitcase up to the baggage shelf on a train. Spreading the weight out works great, and often you have plenty of space to keep at least one piece on the floor in front of you if it isnft a large suitcase. Also, itfs always easier to find coin lockers for smaller pieces.
Because I like to bring home a lot of stuff from Japan, I always check more bags on the way home, by the way. I either bring a fold-up duffel bag or else buy a suitable piece over there. But I have learned to do the bulk of my shopping at the end of the trip (and to allow a couple of days for this) so I donft have to pull out the additional piece while Ifm still traveling around to a bunch of places.
Regarding the JR pass, you probably wonft be able to get a nationwide pass to gpay offh but if you come up with an itinerary that makes it worthwhile, it can be very convenient because if you buy it through the official site you can make JR reservations online up to 30 days in advance, and you can also cancel and change reservations online. For reserved seats on limited express trains and the shinkansen you are supposed to get tickets before you board the train, but typically this takes very little time at the proper machine. (Watch out for Kyoto Station, though. The staffed ticket offices and even the machines can have surprisingly long lines. Except for Kyoto I have never had to wait very long at a machine, but some smaller stations donft have the right kind. And even at Kyoto if you go early in the day the lines tend to be short.) You can use the pass alone (without a seat ticket) to board JR trains only if you use unreserved cars on limited express trains and the shinkansen (or local trains that donft even have seat reservations). But you are going to want to get an IC card for non-JR local transit such as subways and buses. (Read up on IC cards, but basically they are a near-necessity.) There are also some train companies that arenft JR, such as Keihan in Kyoto and Keikyu in Tokyo/Yokohama. You might in fact want to use some of these lines.
As for where to go, I donft think there are any sites in Japan that you absolutely canft miss. I actually consider nearly all the gmust-seeh spots to be gmust-avoidh places because they are almost inevitably seriously crowded, and I donft like crowded places in Japan (to a certain extent you canft avoid them, but I make an effort to). However, for a newcomer I will admit that it is hard to figure out where the great places are that arenft tourist magnets. (I generally wouldnft call them tourist traps, exactly. Places like Hakone, Kinkakuji or Kiyomizudera, and Hiroshima/Miyajima are all okay but can be insanely crowded to the point that they are quite unpleasant.) Ifm sort of with LikeBike on Osaka, although I have a small number of places there that I genuinely like, and I went out of my way to spend one night there on my last trip. It is also not bad as a base for day trips, depending on your itinerary and where your hotel is located. In Kansai I prefer Kyoto as a home base, although I try never to stay there on weekends (room rates go way up, although they also do in Osaka).
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