Randy, I'm sorry to hear that you had a less-than-optimal izakaya experience here in Japan. I don't really know much about life outside Tokyo, but I've been to well over a thousand izakayas here in Tokyo, and I don't think I've ever seen a non-smoking section separated by glass barriers not reaching the ceiling. If there is a non-smoking section, there's usually no barrier at all.

On the other hand, things have gotten much better in the four years since this thread started, and most newly opened shops seem to be non-smoking as the default option. In particular, sake specialty bars are almost always non-smoking. I visited a newish sake bar last month that did allow smoking, and it was kind of shocking to everyone I was with - we all commented on it. That probably wouldn't have been the case ten years ago.

It is certainly not the case that department stores are the only places with non-smoking restaurants. It's also certainly not the case that department store restaurants suck. I've been to many excellent restaurants in department stores, in office-building basements, and in shopping complexes. Again, sorry to hear that you had a bad experience in a department store restaurant, but for the most part they don't suck.

There are already many excellent izakayas that don't allow smoking, and there will be more and more, especially after the laws change next March. There probably won't be a 100% ban on smoking in izakayas, but there will certainly be a huge number of places to enjoy excellent food and drink in a smoke-free environment.

In Koenji, Dachibin is a lot of fun - they serve Okinawan cuisine in a casual izakaya-style setting and sometimes have live music. (https://bento.com/rev/0721.html )

Gyuhachi is a very casual small izakaya under the railroad tracks serving grilled beef on skewers (https://bento.com/rev/4457.html ) There are several similar-looking places surrounding it, but they seem to have the best food that I've found.

Himonoya is a generally reliable chain serving grilled fish that's been dried overnight, and they usually have a good sake list as well (although I haven't been to their Koenji branch yet) (https://bento.com/rev/3923.html )

Citabra, open since March, is the only Koenji craft beer bar worth going to IMO. Their fried chicken is quite good, but I found the rest of the food menu rather disappointing. The beer selection is very good though. (https://bento.com/rev/5339.html )

OK, here are a few of my favorite places to get you started.

Teppen (https://bento.com/rev/4176.html ) in a basement in Otemachi is a great after-work izakaya with good kushiage as well as charcoal-grilled meats and sake.

Rokuhara (https://bento.com/rev/4701.html ) in Akasaka is a bit more upscale for kushiage (deep-fried meat and vegetables on skewers).

Washoku En (https://bento.com/rev/2516.html ) is a great all-around izakaya, with nice views of the city and good food and sake, and it's also close to your hotel.

Hibiki (https://bento.com/rev/3115.html ) is similar in concept, also near your hotel, and also has a great view.

Dedesuke (https://bento.com/rev/4014.html ) in Ebisu has good yakitori, grilled meats and sake. There's also a branch nearer your hotel, in Shimbashi, but it doesn't have quite as much atmosphere IMO.

Shimbashi Yakiton (https://bento.com/rev/4753.html ) is a very casual after-work standing bar serving grilled pork on skewers. You can stand outside or inside, so the smoke shouldn't be too bad, and it's super-cheap. I can't remember if they have English menus though.

Torisuki (https://bento.com/rev/4924.html ), located in a shopping mall in Ginza, has fantastic grilled chicken and game birds and rather refined, Kyoto-style side dishes.

There are probably tens of thousands of izakaya in Tokyo (and nearly all of them are better than the places in Piss Alley), so it would help to know what neighborhood you'll be in, and what kind of food you like. Some izakaya are good for raw seafood, some for charcoal-grilled meats, some for chicken on skewers, some for pork, some for deep-fried dishes, and many have regional specials. Also, do you mind cigarette smoke?

Here are some places in Tokyo with good sake lists (although note that not all of them are traditional izakaya style). https://bento.com/dbinx/r-sake.html

For yakitori, here are a few non-smoking shops that I particularly like. I don't know about their policies towards children, so you'll have to check.
Torisuki in Ginza is good with the game birds: https://bento.com/rev/4924.html
Souten in Otsuka, also strong in the game-bird department: https://bento.com/rev/3265.html
Torisen in Mitsukoshimae has a separate smoking section, and also a private room as I recall: https://bento.com/rev/5245.html
I haven't been to Torikou in Ebisu, but it looks promising, has a nice view, and is close to Naka-Meguro: https://bento.com/rev/4982.html

I will second the idea of spending the day in Kichijoji. There's a small zoo in Inokashira Park that's quite nice, specializing in animals native to Japan, and there's a small-bird cafe called Kotori Cafe that might be fun. The shopping streets north of the station are lively but manageable.

I'll also second shakti2's suggestion to not discount restaurants and izakayas in department stores (and shopping malls). Some of them are very good, and they tend to be much more geared towards serving diners with young children, generally equipped with high chairs, coloring books, juice boxes and so on.

(And if you want to go to regular izakayas, I'd suggest going very early, e.g. as soon as they open at 5 or 5:30pm, before they start getting too smoky.)

You've done a lot of work! This looks more sensible than 90% of the itineraries posted here. Just a few comments:

Day 2
- I think Onibus Naka-Meguro is all outdoor seating, no? If so, be sure to dress warmly.
- In my experience, Kushiwakamaru has always been pretty smoky. And always pretty full.
- Also, you can get your photo of Hachiko while you're in Shibuya - it's a few minutes away from Magnet by Shibuya 109 Roof.

Day 3
- There's a branch of Butagumi called Butagumi Shokudo that's right in Roppongi Hills - that might be more convenient than the main branch.

Day 5
- You probably know this already, but just in case you didn't, teamLab Borderless is closed on the second and fourth Tuesdays of the month.

Day 6
- Kichijoji has a pretty big park of its own, and since you'll already be there it might be worth checking out.

I know you mean well, but this suggestion of an "allergy card" comes up nearly every time someone mentions allergies during a trip to Japan, and it's never helpful. The minimum-wage part-time serving staff at your restaurant is not equipped to deal with your special dietary requirements, and whether or not they "alert the kitchen staff" in the middle of dinner rush, it's not going to help much, unless you happen to be in a restaurant in an international hotel (in which case you don't need the card anyway).

The kitchen staff may very well have no idea which dishes contain wheat or soy, and the serving staff at your restaurant might not even be able to read Japanese.

The epi-pen is a good idea though.

It's great that you're doing so much advance planning! Just a few comments on your questions.

- "I have found a restaurant in Shinjuku called Seryna which claims to have Kobe beef as part of their shabu shabu set course menu" - Seryna is pretty well known, and I would assume that they're telling the truth. However "Kobe beef" is just one of a dozen or so well-known types of branded wagyu (such as Matsuzaka beef), and it's worth looking at other types as well, since they're of similar quality. (Kobe beef is simply the one that's been most successful at marketing in other countries.)

I've had excellent-quality, reasonably priced steaks at some restaurants in Kobe that were otherwise pretty mediocre - iceberg-lettuce salads with bottled French dressing, supermarket wine served in a tumbler - so there's more to look at than just the meat when you're picking a place. Personally if I'm eating fancy wagyu I'd much rather have a steak (even a tiny one) than shabu-shabu (where the flavor gets washed out), sukiyaki, or yakiniku (which is generally served with Korean-style side dishes).

- Obanzai-ryori is a distinctive regional cuisine that's local to the Kyoto area, and as Notti says it's based on home-style dishes. I've seen it served in izakaya both in Tokyo and Kyoto, and it fits in well with izakaya-style dining since it's all small dishes. Sorry I don't have any recommendations for Kyoto (my favorite two places have closed down), but I think it's worth checking out.

- Depachika are fantastic for buying prepared gourmet foods to bring home (or to your hotel room). Some of them also have little restaurant stalls as well as take-out kiosks, but in my experience the restaurants located in depachika are nothing special, and usually pretty average. Generally any department store with a depachika in the basement will also have a restaurant floor on the top floor, and these tend to have casual, reasonably priced restaurants of decent quality.

- For Kyoto kaiseki, I really enjoyed lunch at Roan Kikunoi - it's really fantastic food, it doesn't take forever, it's not too formal, and you sit at a spacious counter with other people. It's also quite reasonably priced. https://bento.com/kansai/rev/7108.html

- For tofu in Kyoto, I really like Komameya (a yuba specialist), and shojin-ryori restaurants like Shigetsu and Izusen. You won't go wrong with any of these IMO. https://bento.com/kansai/kc-kyoryori-...

- Izakayas are just places that serve drinks and food to go with the drinks, and they come in many styles. Some izakaya specialize in yakitori, and these are called yakitoriya. Some izakaya serve yakitori and lots of other dishes. Some izakaya might specialize in seafood, and not serve yakitori at all. If you really like yakitori, it might be worth checking out places that specialize in it - there's often quite a difference in quality between ordinary izakaya and specialty yakitoriya.

- Generally speaking when I'm traveling around in Japan I like to go to izakayas at night, and try out more specialized cuisines (tempura, unagi, tonkatsu, gyukatsu, etc.) during the day. Most places are pretty comfortable for solo diners at lunchtime, especially if you arrive after 1pm. In the evening anyplace that has a counter will be very welcoming to solo diners.

- You can definitely get kakigori in early spring, you just have to go to a place that serves it all year round. Some places to look for are Minatoya in Sasazuka (http://bento.com/rev/4747.html ), Shimura in Mejiro, Himitsudo in Nippori, and Darumaya in Jujo.

- For omurice my favorite spots are Mantenboshi in Marunouchi, Azabu Shokudo in Nishi-Azabu, and the very old-fashionied Tsuitsui in Kayabacho (http://bento.com/r-yoshoku.html ).

- For tonkatsu, there's a whole devoted thread or two elsewhere on Chowhound with a lot of recommendations.

In Kyoto, El Fagon is good for Spanish: http://bento.com/kansai/rev/7128.html

Sarasa 3 has a nice atmosphere and a good range of Mediterranean cuisine: http://bento.com/kansai/rev/7132.html

Il Ghiottone prepares Italian dishes using Kyoto heirloom vegetables and other local ingredients: http://bento.com/kansai/rev/7069.html

In Osaka at lunchtime, I like the casual regional French (Bretagne) cuisine at Amelie: http://bento.com/kansai/rev/8219.html

>what I also love is the fact that Japan is one of the few places where French food, for example, is probably even better than in France.

Maybe not in Kyoto though - it's really all about the Japanese food there. Tokyo and even Osaka are much more international.

Traditionally sake was not drunk at the same time as sushi - you would drink sake with your starter otsumami, sashimi and so on, then switch to beer or tea when it came time for the sushi. Although nowadays this isn't very strictly followed, in my experience sometimes the chef has asked if it's okay to move onto the sushi course if you're still drinking sake.

I generally just order some sake that I like, then when I finish that I will get a different sake that I like, and sometimes I will ask for advice. I don't think the concept of "pairing" goes particularly well with sushi since there are so many distinctively flavored items arriving in succession.

The local sushi shop I go to has a fairly nice sake list with seasonal specials, but many sushi-shop sake lists are rather run of the mill. The last time I went to a super-high-end sushi place the menu only listed one brand of sake, and the chef explained that he chose something very neutral because he didn't want it to compete with the flavors of the fish. So I guess that's a thing.

Anyway, I would advise just ordering sake that you like (or maybe asking for recommendations) and drinking it at your own pace.

Izakayas are, by definition, drinking spots, so they don't tend to be open during the day, although sometimes they will have a very abbreviated menu for a lunchtime crowd. The few izakayas that are open in the early afternoon tend to cater more to daytime drinkers, and are more focused on cheap drinks rather than good food.

In general your best chance of finding non-ramen restaurants open between 2-5pm is inside department stores and shopping malls (like the Atre malls that can be found at many JR stations).

OK, I don't know about grab and go meals, I always just buy things and take them home, but my favorite depachikas are probably Isetan (Shinjuku), Hikarie (Shibuya), FoodShow (Shibuya), and Mitsukoshi (Ginza). Isetan is probably the most upscale and interesting (as opposed to Takashimaya which is upscale but less interesting).

Seibu (Ikebukuro) is the biggest in town, and it's connected to another massive depachika called ISP right next to it, so that's definitely worth a visit if you're in the area.

My favorite karaage shop in the world is in Marunouchi, just across the tracks from your hotel! It's called Tokyo Karaage Bar, and you can not only choose from different dipping sauces (shallot tartar, yuzu kosho, spicy Death Salsa), but you can also choose which cuts of chicken you want - wings, leg, breast, gizzards, bonjiri (chicken tail), etc. http://www.bento.com/rev/4613.html

There's also a "fun" yakitori shop just next to Tokyo Karaage Bar, (in the same basement), called Abeya. They serve an heirloom-breed chicken from Akita Prefecture called hinai-dori, along with Akita sake. http://www.bento.com/rev/4611.html

For tonkatsu, I'd recommend Agezuki in Kagurazaka and Butagumi Shokudo in Roppongi Hills. Narikura in Takadanobaba is very good, but it might be a long wait on line. There are a few threads specifically about tonkatsu in Tokyo here on Chowhound.

I'm not familiar with torikatsu - is it a regional thing?

As for monjayaki, IMO it's just a less-appealing version of okonomiyaki, so why not go for okonomiyaki instead? Although En Okonomiyaki in Kagurazaka does both, so I guess you can compare. Sakuratei in Harajuku also does both. For straight-up okonomiyaki I like Oshio in Tsukishima, although I probably couldn't tell the difference between there and fifty other shops in that neighborhood if I were blindfolded.
http://www.bento.com/r-takoyaki.html#...

For udon, my top B-kyu choices would be the curry udon at Norabutaya in Yotsuya, the cold tomato and cheese udon at Atsumaru in Ogawamachi, and any of the cream-sauce and seafood udon bowls at Tsurutontan in Ginza. http://bento.com/r-udon.html