What to do in Tokyo, decided for you
The honest answer isn't a list of forty things. It's fewer things, in the right order.
Search this question and you get a list of forty attractions, ranked by nothing in particular, written by somebody who spent four days here. The people who enjoy Tokyo most do the opposite of that list. They pick two or three areas, walk them properly, eat where they end up, and go back to the hotel before they're wrecked. Tokyo isn't a city of sights with gaps between them. The gaps are the city. That's why everything here is organised by area rather than by attraction, and why there are 245 walks you can watch before you go anywhere.
Pick an area, not an attraction
An attraction takes an hour and leaves you standing on a pavement wondering what's next. An area takes an afternoon and answers that question by itself. Asakusa is a temple, a shopping street, a river and about forty places to eat, all within ten minutes of each other. Shinjuku is a station, two nightlife districts and a garden. If you plan by area, the day fills itself and you stop losing forty minutes to the train every time you change your mind.
The day splits in two, and most people only plan half of it
Tokyo at two in the afternoon and Tokyo at nine at night are different cities in the same postcode. Markets and gardens are a morning thing and genuinely over by early afternoon. Golden Gai at four is a shut alley; at ten it's the reason people come. Plan one daylight area and one after-dark area and you've got a full day without rushing either. Plan two daylight areas and your evening turns into a convenience store sandwich in the hotel.
What actually deserves a queue
Very little. The queue is usually the price of a photograph you've already seen, and the same street two blocks over is empty and better. There are exceptions, and they're mostly food: places with eight seats and one thing on the menu are worth standing for, because there's no second branch and no way around it. A viewing platform is not worth an hour of your one evening. The view from a free hotel bar on the forty-something floor is the same city.
When it rains, and when you’re finished
It will rain, and you will be more tired than you planned for, usually on day three. Both are solvable if you decide in advance rather than on the pavement. Rain moves you underground and indoors: station complexes, department store food halls, covered shopping streets that run for blocks. Tiredness moves you to one area and keeps you there. The trips that go wrong are the ones with no fallback, where a wet afternoon costs you a whole day of arguing about what to do instead.
What to do in Tokyo: common questions
How many days do you need in Tokyo?
Three gets you the shape of the city. Five lets you have a slow day without feeling like you wasted one, which matters more than it sounds. Beyond a week you'll want a day trip or two, not more Tokyo.
What should I do on my first day?
Something flat, compact and close to your hotel, because you'll be more jet-lagged than you expect. Asakusa is the usual right answer: it's interesting from the first minute and it doesn't need a plan. Save the big stations for day two, once the trains make sense.
Is Tokyo expensive to visit?
Getting here and sleeping here are expensive. Being here is not. Eating well costs less than most European capitals, a lot of the best of the city is a street you walk down for nothing, and the trains are cheap. The budget page goes through where the money actually goes.
What do I need to book in advance?
Almost nothing, with two exceptions: the small counter restaurants that seat eight or ten, and anything with a timed entry. Everything else you can decide on the morning, which is the pleasant thing about the city.
What is the most common mistake?
Cramming. Four areas in a day means four train journeys, four sets of station exits and no time in any of them. Two is the number that works, and the second one should be after dark.