1. Earthquakes and tsunamiAround 20% of the World's large earthquakes (over magnitude 6) happen in Japan. Japan is probably the most earthquake resistant country due to engineering standards. However, no amount of engineering can make a large earthquake safe.
Small and moderate earthquakes can almost be an interesting experience. In a quiet year there are 3 or 4 noticeable earthquakes in Tokyo. When there's a big event such as the tragic 2011 Tohoku Earthquake — a given area may experience 100s of earthquakes.
2. Too many nerdsJapan's otaku pop culture attracts nerds from far and wide.
3. EnglishJapan isn't an English speaking country. As a tourist it's a good idea to learn a few words of basic Japanese. If people are nice enough to speak English to you — speak slowly.
4. Too many trainsJapan is a train-centric culture. This can be a change for people from a car-centric culture. If North America looks like this.
Japan looks like this.
It's not recommended to use cars for urban or intercity travel. For die-hard road trip enthusiasts — the best place to drive is in the countryside.
5. Everything is too cuteIn recent years, kawaii has become the most popular Japanese aesthetic.
6. Rainy SeasonIn much of Japan, summers are rainy and hot. The official rainy season varies by location.
7. Nightlife is too goodTokyo nightlife is so good that some people forget themselves and take things a bit too far. There are 7 levels of Tokyo nightlife success.
8. Long lines for ramenJapan's restaurant market is extremely competitive. There's a trendy aspect to it. If a restaurant gets a few good reviews it will have long lines. The shop next door may be completely empty.
Long lines are most common for B-class gourmet foods like ramen. The dilemma for the traveller is to join or not to join (the long lines). Locals will tell you that exceptional B-class restaurants are worth the wait.
9. NudityOnsen are one of the best reasons to visit Japan. They generally require nudity — this can represent culture shock for shy foreigners.
Onsen has several rules of etiquette that you need to learn before trying it. Otherwise, you risk being embarrassed.
10. The Right WingJapan has several extreme right wing groups that regularly demonstrate in Tokyo. They're easy to spot in their militaristic looking black trucks and buses. If you run into the right wing don't get involved. It's also not recommended to photograph them at close range. They've been known to attack photographers.
The Tokyo Metropolitan Police usually come out in force for a big right wing demonstration.