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Is there a reason you prefer that one? I was looking at Hyperdia, which seems like it does the same thing. What caught my eye about it in the blogs/reviews I've read is that it has train search features that let you find only the routes and trains that accept the JR Pass, which is how we plan on doing most of our getting around. Does Navitime have a comparable feature?
Yes, Navitime lets you prioritize JR Pass routes, so you’ll be able to select your preferred route. My DH said he chose Navitime over Hyperdia because he’d read reviews that said Navitime did a better job of keeping up-to-date about closures, etc. otherwise, they’re very similar.
 
We spent five full days and a couple half days in Tokyo. Three to four days for the city is plenty IMO. We had two day trips planned from Tokyo. One to Fuji, but that fell through. The other was north towards Nagano to see the Jigokudani snow monkeys. That was a much better experience than the Kyoto monkeys, which was crowded and had a circus-like vibe. The monkeys at Jigokudani are the world famous onsen-soaking troop that are often featured in nature documentaries. It would take more time to do and requires a moderately difficult walk up a mountain, but it’s definitely the more rewarding experience of the two. So if you have the time and interest, that’s the one I would recommend.

We based ourselves in Kyoto for five nights, I believe? Two full days for Kyoto — how much time you spend there depends on your interest level for history and temples. I’m sure some people would love to explore every single one; I was happy to just see a few. We daytripped from Kyoto to Hiroshima/Miyajima one day, another day we did a day trip to Nara. I think the latter would appeal to your younger daughter. It’s overrun with semi-tame deer that bow to you when you feed them, and the Todaiji Temple has the giant Buddha where she can try squeezing through his nostril to achieve eternal salvation (or something to that effect. It’s been a while since I did it.)

The trains are incredibly efficient and timely and do not eat up as much time as public transportation does in the US. They’re also not as difficult to navigate as you might expect. Download the Navitime app.

The bowing deer are definitely a must-see. My daughter took pictures of some at Miyajima that are just precious! Her 10yo host sister was feeding them to get them to bow, and there were a couple just waiting outside of the door to a building (temple?) for people to come out.

The onsen monkeys sound adorable, and less crowded/circus-like is always a plus. I'm hoping to have a day to check out the area around Nagano, but time will be the deciding factor there. I'd actually love to venture further into the northern part of the country - there are a few things in Akita prefecture that looked interesting to me, and Hokkaido looks incredibly beautiful - but since the most important stop on the trip is Shimane, it seems like it makes more sense to focus on the area between there and Tokyo.

Figuring out travel time and method is definitely one of the bigger challenges of planning a trip like this for me. We don't have public transportation to speak of in my area, and while I enjoy traveling by train, I'm used to it being a couple of scheduled departures per day to choose from with tickets purchased almost as far in advance as plane fares. The Japanese train system looks more like what I'd expect from a subway system, in terms of the frequency of trains on the routes I've looked at so far, and I was really surprised to find some itineraries that call for taking a morning train to the station nearest a particular point of interest (Himeji Castle was one I remember) and then catching an afternoon train on to the next city. And the speed of the shinkansen is hard for my road-tripper's brain to comprehend - Amtrak from Detroit to Chicago takes about an hour and a half longer than driving, and I've done that trip often enough by both methods that it is my mental benchmark. But when I looked it up, even the non-express shinkansen that the JR Pass includes takes less than half as long as it would to drive from Tokyo to Kyoto!

I'm also dreading the parts of the trip where I'm going to have to drive. Between a language barrier on the road signs and having to learn to drive on the wrong side, that part is nerve-wracking. But a couple of the places we're going are far enough off the beaten path that public transportation is sparse or very inefficient so I'm going to have to get my international drivers license and tough it out with a rental car.
 
Yes, Navitime lets you prioritize JR Pass routes, so you’ll be able to select your preferred route. My DH said he chose Navitime over Hyperdia because he’d read reviews that said Navitime did a better job of keeping up-to-date about closures, etc. otherwise, they’re very similar.
I downloaded both and the HYPERDIA app told me I have to pay after 30 days. I ended up deleting it. I like the look of the Navitime app more anyway.
 
The Japanese train system looks more like what I'd expect from a subway system

The local / metro trains can be pretty overwhelming at first. The train stations themselves can be the size of small underground cities. If you can, I'd recommend using Google maps. It tells you the next train to your destination and the platform number. That makes it a bit easier than trying to decipher the electronic timetable displays which obviously list a lot of information because there are a lot of trains.

For the bigger journeys, we always like to reserve seats using the JR Rail Pass the day before. It's a good way to decide on departure and return times and the person in the ticket office normally is able to communicate in basic English if you have any queries. Visiting more than one city on the bullet trains is definitely doable and something that we have done multiple times.
 


The local / metro trains can be pretty overwhelming at first. The train stations themselves can be the size of small underground cities. If you can, I'd recommend using Google maps. It tells you the next train to your destination and the platform number. That makes it a bit easier than trying to decipher the electronic timetable displays which obviously list a lot of information because there are a lot of trains.

For the bigger journeys, we always like to reserve seats using the JR Rail Pass the day before. It's a good way to decide on departure and return times and the person in the ticket office normally is able to communicate in basic English if you have any queries. Visiting more than one city on the bullet trains is definitely doable and something that we have done multiple times.

Thanks. I will definitely be renting a pocket wi-fi to have service while we're there, so Google Maps will probably get a lot of use. I am also going to download one of the transit apps mentioned up-thread - I think I need to do what @Haley R did and download them both to decide which I like better.

I've heard good things about the English abilities of a lot of public-facing workers in touristy places, but we also have some basic ability to communicate in Japanese. Mine is conversational at best, but my daughter has had two years of high school Japanese, eight weeks of living there, and by the time we leave, probably another year of college-level classes. So I'm not too terribly worried about communication except in some of the more rural places we're visiting.
 
The bowing deer are definitely a must-see. My daughter took pictures of some at Miyajima that are just precious! Her 10yo host sister was feeding them to get them to bow, and there were a couple just waiting outside of the door to a building (temple?) for people to come out.

The onsen monkeys sound adorable, and less crowded/circus-like is always a plus. I'm hoping to have a day to check out the area around Nagano, but time will be the deciding factor there. I'd actually love to venture further into the northern part of the country - there are a few things in Akita prefecture that looked interesting to me, and Hokkaido looks incredibly beautiful - but since the most important stop on the trip is Shimane, it seems like it makes more sense to focus on the area between there and Tokyo.

Figuring out travel time and method is definitely one of the bigger challenges of planning a trip like this for me. We don't have public transportation to speak of in my area, and while I enjoy traveling by train, I'm used to it being a couple of scheduled departures per day to choose from with tickets purchased almost as far in advance as plane fares. The Japanese train system looks more like what I'd expect from a subway system, in terms of the frequency of trains on the routes I've looked at so far, and I was really surprised to find some itineraries that call for taking a morning train to the station nearest a particular point of interest (Himeji Castle was one I remember) and then catching an afternoon train on to the next city. And the speed of the shinkansen is hard for my road-tripper's brain to comprehend - Amtrak from Detroit to Chicago takes about an hour and a half longer than driving, and I've done that trip often enough by both methods that it is my mental benchmark. But when I looked it up, even the non-express shinkansen that the JR Pass includes takes less than half as long as it would to drive from Tokyo to Kyoto!

I'm also dreading the parts of the trip where I'm going to have to drive. Between a language barrier on the road signs and having to learn to drive on the wrong side, that part is nerve-wracking. But a couple of the places we're going are far enough off the beaten path that public transportation is sparse or very inefficient so I'm going to have to get my international drivers license and tough it out with a rental car.
The trains there are more akin to what subway systems are for us, just faster, cleaner, and more reliable. Lol.

I bought my first train ticket while still at Narita airport after landing in Japan. The woman handed me the ticket and said the train leaves in three minutes. I was dumbfounded, wondering why this woman would sell me a ticket for a train I couldn’t make. I told her I couldn’t make it, she told me I had plenty of time, we went back and forth a bit. I was asking where I needed to go and she just kept saying “take the escalator” but wasn’t telling me where to go after that. So I turn around, go up the escalator, and walk directly through the open doors onto the train waiting at the top... because the train had been overtop my head the whole time and I didn’t know it. So yeah, train travel over there is much more accessible than what we’re used to here.

“World’s Busiest Train Station: Shinjuku” is a fascinating documentary. Check it out when you get the chance.
 
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Thanks. I will definitely be renting a pocket wi-fi to have service while we're there, so Google Maps will probably get a lot of use. I am also going to download one of the transit apps mentioned up-thread - I think I need to do what @Haley R did and download them both to decide which I like better.

I've heard good things about the English abilities of a lot of public-facing workers in touristy places, but we also have some basic ability to communicate in Japanese. Mine is conversational at best, but my daughter has had two years of high school Japanese, eight weeks of living there, and by the time we leave, probably another year of college-level classes. So I'm not too terribly worried about communication except in some of the more rural places we're visiting.
I haven't decided yet about renting a Mifi. We have Tmobile and I'm pretty sure we have international data. That's definitely something I need to figure out before we go. We will probably still rent a Mifi anyway. It looks like with Tmobile we do have free unlimited international data in Japan, but it looks spotty on the map. I'm not sure if the Mifi is better, though?
 


I haven't decided yet about renting a Mifi. We have Tmobile and I'm pretty sure we have international data. That's definitely something I need to figure out before we go. We will probably still rent a Mifi anyway. It looks like with Tmobile we do have free unlimited international data in Japan, but it looks spotty on the map. I'm not sure if the Mifi is better, though?

We're with a discount carrier, so I'm not planning on adding international calling to our plan. I'm not even sure that I can, actually. I know they offer Canada and Mexico coverage but I think that's it. I can add packages to allow me to call foreign countries, but not to provide service there. I'm okay not having phone service for the trip, though; my girls and I can communicate via FB messenger or Line, and it would actually be rather nice to have a few weeks without work calls.

The consensus on the pocket wifi seems pretty good among travel bloggers, but I am still searching for more reviews and experiences outside of the Tokyo-Kyoto-Osaka area of the country. My daughter said public wifi is more available than a lot of the travel sites make it sound too, which is probably related to the Japanese govt's pre-Olympic push to improve travel amenities, though it certainly isn't available everywhere like it is here.
 
We're with a discount carrier, so I'm not planning on adding international calling to our plan. I'm not even sure that I can, actually. I know they offer Canada and Mexico coverage but I think that's it. I can add packages to allow me to call foreign countries, but not to provide service there. I'm okay not having phone service for the trip, though; my girls and I can communicate via FB messenger or Line, and it would actually be rather nice to have a few weeks without work calls.

The consensus on the pocket wifi seems pretty good among travel bloggers, but I am still searching for more reviews and experiences outside of the Tokyo-Kyoto-Osaka area of the country. My daughter said public wifi is more available than a lot of the travel sites make it sound too, which is probably related to the Japanese govt's pre-Olympic push to improve travel amenities, though it certainly isn't available everywhere like it is here.
I doubt Dh and I will use calling at all. Tmobile gives us free texting and data internationally it's just at a 3G speed so it might be slow. For part of our trip we are staying at an Airbnb that provides a Mifi. We might stay in one in Kyoto that also has a Mifi provided. We will mainly just need to rent one for our Disney part of our stay.
 
You got some good advice on other parts of your trip so I'm just going to comment on Hokkaido & Kyushu.

You can absolutely do either or both as part of a three-week trip but you are going to want to fly. Is that something you'd feel comfortable doing? For example, from Tokyo, Sapporo is about a 2 hr flight or an 8 hr train ride. Some people just do not want to fly domestically within a destination and that is fine, but I don't think I would opt for a 16 hour round trip train ride. If you make it up there, though, it's beautiful.

Public wifi remains spotty & unreliable. It's better than it was, but it's not great. When I was a student/visitor & therefore didn't have "real" phone service, I dragged my poor old PuPuRu wifi everywhere and it had service even in rural Shizuoka & Miyazaki.
 
Yes, Navitime lets you prioritize JR Pass routes, so you’ll be able to select your preferred route. My DH said he chose Navitime over Hyperdia because he’d read reviews that said Navitime did a better job of keeping up-to-date about closures, etc. otherwise, they’re very similar.
I love the Navitime app! It has some really good articles that I've been saving and typing up notes from.
 
You got some good advice on other parts of your trip so I'm just going to comment on Hokkaido & Kyushu.

You can absolutely do either or both as part of a three-week trip but you are going to want to fly. Is that something you'd feel comfortable doing? For example, from Tokyo, Sapporo is about a 2 hr flight or an 8 hr train ride. Some people just do not want to fly domestically within a destination and that is fine, but I don't think I would opt for a 16 hour round trip train ride. If you make it up there, though, it's beautiful.

Public wifi remains spotty & unreliable. It's better than it was, but it's not great. When I was a student/visitor & therefore didn't have "real" phone service, I dragged my poor old PuPuRu wifi everywhere and it had service even in rural Shizuoka & Miyazaki.

I would prefer not to fly, which is the biggest reason why I'm leaning toward not doing Hokkaido. But I am still waffling because it does look so very beautiful. I'm a terribly nervous flyer, though, and I have an especially hard time with short flights/small planes - a 737 is really the smallest I want anything to do with. So I'm trying to work out an itinerary that sticks to the trains. From that angle, Kyushu seems so much easier based on our other destinations - 3.5 hours by train from Hiroshima to Kagoshima rather than the 9 hours from Tokyo to Sapporo.
 
“World’s Busiest Train Station: Shinjuku” is a fascinating documentary. Check it out when you get the chance.

That really was fascinating and a little terrifying! I thought the Metro during inauguration weekend was bad, but OMG, that's nuts! I'm almost glad we have decided not to bring DH along on this trip - he has some anxiety issues with crowds, to the point of not being able to deal with Disney fireworks on busier days, and that would be too much for him. (He also has a life-threatening fish allergy, which is why DD suggested he stay home; cooking with her host families, she was amazed how many "hidden" fish products there are in seemingly non-fish dishes).

I doubt Dh and I will use calling at all. Tmobile gives us free texting and data internationally it's just at a 3G speed so it might be slow. For part of our trip we are staying at an Airbnb that provides a Mifi. We might stay in one in Kyoto that also has a Mifi provided. We will mainly just need to rent one for our Disney part of our stay.

I noticed that a lot of AirBnB accommodations include them. When you get back, you'll have to let us all know how that works out for you. I'm torn between taking advantage of what is provided (I think the places I'm looking at in both Tokyo and Kyoto include a pocket wifi) and going with the ease of having a single device for the entire trip.
 
That really was fascinating and a little terrifying! I thought the Metro during inauguration weekend was bad, but OMG, that's nuts! I'm almost glad we have decided not to bring DH along on this trip - he has some anxiety issues with crowds, to the point of not being able to deal with Disney fireworks on busier days, and that would be too much for him. (He also has a life-threatening fish allergy, which is why DD suggested he stay home; cooking with her host families, she was amazed how many "hidden" fish products there are in seemingly non-fish dishes).



I noticed that a lot of AirBnB accommodations include them. When you get back, you'll have to let us all know how that works out for you. I'm torn between taking advantage of what is provided (I think the places I'm looking at in both Tokyo and Kyoto include a pocket wifi) and going with the ease of having a single device for the entire trip.
I’ll definitely report back. We won’t be getting one single mifi the entire trip because we have one Airbnb for sure that will have one for us in Tokyo.
 
I would prefer not to fly, which is the biggest reason why I'm leaning toward not doing Hokkaido. But I am still waffling because it does look so very beautiful. I'm a terribly nervous flyer, though, and I have an especially hard time with short flights/small planes - a 737 is really the smallest I want anything to do with. So I'm trying to work out an itinerary that sticks to the trains. From that angle, Kyushu seems so much easier based on our other destinations - 3.5 hours by train from Hiroshima to Kagoshima rather than the 9 hours from Tokyo to Sapporo.
I would give Hokkaido a pass, then. No sense putting yourself through that kind of anxiety on vacation. Kyushu is a nice side trip & definitely worth the time to get out there.
 

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