In short
Tokyo has no centre: it is a constellation of station districts, each with its own density and character, strung along the Yamanote loop.
Shinjuku is the busiest railway hub in the world and the nightlife quarter. Shibuya is young and commercial. Shimokitazawa and Koenji are the vintage-shop and small-bar districts. Yanaka and Kagurazaka have kept the scale of old Tokyo. Chiyoda holds the imperial palace and the offices.
You do not visit Tokyo; you visit five or six districts and give up on the rest.
Arriving and getting around
Two airports. Narita is sixty kilometres out — Narita Express or Keisei Skyliner, an hour. Haneda is much closer, twenty to thirty minutes by monorail or the Keikyu line.
A Suica or Pasmo card is essential: it works across every operator, on buses, and in most convenience stores.
The network mixes JR, Tokyo Metro and Toei subway: these are different companies, and switching between them mid-journey means paying a new fare. Apps show this, paper maps less so.
The last train runs around midnight and there is no night service: missing it means an expensive taxi or a night out.
What it really costs
Tokyo is cheaper than its reputation on food: teishoku set meals, konbini and noodle chains serve very decently for a few euros.
Accommodation is the dominant item, and the rooms are small.
When to come
March–April for the cherry blossom, October–November for the maples: these are the two peaks of crowding and price. May and early June are mild and quieter.
June–July is the rainy season, August is hot and very humid, and September remains exposed to typhoons.
What nobody tells you
Many small establishments take cash only, including well-regarded restaurants. Konbini cash machines accept foreign cards, unlike many bank ones.
Public bins are all but non-existent: you carry your rubbish until you reach a station or a konbini.
Eating while walking is frowned upon, and so is speaking on the phone on public transport.
Tattoos remain prohibited in many onsen and public baths. Some places accept them if covered, others do not.