One well-received and much commented-on blog post I wrote many years ago covered the "stages of living in Japan". These are the 5 stages I have witnessed, again and again, in myself and in others, and though your mileage may of course vary, they seem pretty spot on. I daresay they could be applied to living in any country.
Green stage, "The Tourist"
Wide-eyed amazement, the big screens in Shibuya, the toys, the people, the clean and punctual trains.
LeafGreen, "The Honeymoon"
You've just moved here, life is good and exciting. You're learning new things every day.
Orange, "The Hangonaminute"
Culture shock creeps in. "What do you mean I can't order extra mayonnaise?" "How many times do I have to fill out the same form??"
Red, "Mr. Angry"
Aggression. The trains are too crowded. Salarymen stink. People are not friendly at all, just very annoying and unaware of others. No one speaks English one tiny bit after 6 years of mandatory study at school. Some things are way too expensive. Tokyo is dirty. Mental isolation. Pure hatred! Rampant racism and xeno-ignorance.
Grey, "The Realist"
Acceptance. Hey, Japan is a country pretty much like every other country in the world. It has good points, bad points, nice people and arseholes. Live with it.
The progression through these stages may go faster or slower depending on how much you want to buy into Japan's cultural myths, or how much you expect to be able to integrate. If people leave the country to go back home while in the Orange stage they will continue to think of Japan as a crazy, obtuse and weird country. People who leave during the Red stage, when temptation to throw in the towel is the most severe, will end up bitter and twisted, ranting with hatred to anyone nearby.
Once you reach the Grey stage you may occasionally find yourself slipping back into earlier stages for a while. During a nice holiday in the countryside, for example, you may be reminded of Japan's friendliness and general helpfulness, or during a bad period at work or a packed commute you may slip into hatred again.
The thing to remember is that no matter how special you thought Japan was, like everywhere else, it has good points and bad points, and your enjoyment of life here entirely depends on how you deal with either and if the balance for you personally is in favour of the good.
"The Japanese are so polite."
The Japanese certainly like to think they own the patent on communal respect, empathy and "wa", the social glue that keeps everything flowing harmoniously. Sadly, there doesn't seem to be a gene that makes people polite that is in every Japanese person's make up. Japan, like every other country in the world is filled with both wonderful people and utter idiots.
Though there is certainly an element of trying not to make too many waves, not trying to be too difficult if it can be avoided, this often manifests itself in a disregard for your immediate surroundings. People pretend to be sleeping in the train's priority seats when a pregnant or old woman has to stand, they read broadsheet newspapers when there is no space, they talk loud in quiet streets in the middle of the night. In short: Japan is like every country in the world.
Just because there are fairly rigid rules of conduct in strong social hierarchies doesn't mean the Japanese are automatically more polite or respectful of others. It just sometimes may seem that way.
"Japan is safe."
Japan is safer than what you're used to maybe. I have little qualms walking around with wads of cash, leaving my bag on a seat while I go get some coffee and get drunk in pubs without it ending in physical violence. However, crime does happen, it just isn't reported as much.
Sometimes in the seedier areas you may encounter pickpockets, fall victim to a roofie, have your credit card abused, be tricked into extortionate "table seating" fees. You still need to stay alert. Generally, though, you can relax a bit compared to back home, just don't think it's a "leave the door unlocked at night" kind of country.
"Japanese food is healthy."
Some Japanese food is healthy, just as some English food is healthy and some American food is healthy. Japan has its fair share of junkfoods, fatty cheap fare that, when overindulged in, can cause the same kind of spare-tire blubber as, say, Western fast foods and such.
It is true that Japanese cuisine has a lot of excellent and healthy dishes that are both tasty and awesome! If you stick to a (healthy) Japanese diet you may see all manner of life-prolonging health changes. Live a life of convenience store onigiri and bentos, though, like a true game developer, and don't be surprised to be sweating grease like a fat hog before too long. Together with Japan's embrace of alcohol you might even find yourself gaining weight when you first move to Japan!
"The Japanese love Western stuff and people!"
They sort of do, but it's not a hard and fast rule. A lot of Western culture makes its way to Japan, but is passed through some filter, coming out the other side slightly odd and different. Pizzas with wasabi and mayonnaise, sandwiches with whipped cream and strawberries and mayonnaise, cocktails with sake and mayonnaise, everything gets a slight adjustment to make it appeal more to the Japanese, who really do seem to like their mayonnaise.
Similarly people; some Westerners are a-okay, especially the Caucasian English-speaking types from recognizable major cities. Other races from different locales aren't as openly adored. Even then, there will be plenty of people who will detest you for being "cooler" or being considered "cooler" or getting an easy ride—and despite our problems, most Westerners do get an easy ride.
Social life in Japan
Social isolation might become a real issue, even for the most extroverted ex-pats.
Though plenty of Japanese will be friendly with you, colleagues or strangers in bars, and you'll be asked out many times you will find the connections you make will fall short of true friendships most of the time. In Japan, like almost everywhere, your true friendships are forged during your formative and college years and by the time you burst onto the scene in your colleagues' social lives they will already be settled in their own circle of friends.
Some will come to regard you as their "foreign friend". You might get invited to wedding parties and drinking engagements and be presented as a friend of the organizer, merely so his or her friends can be impressed they have foreign friends. It is not a bad situation to be in, just don't mistake it for true friendship.
The Japanese are notorious drinkers and will often get drunk beyond decency at any occasion. These can be fun times and often stuffy colleagues let their guard down. You may be surprised, though, that the very next day things will be back to normal at the office, and the drunken conversations about deeply personal issues had the night before will now be ignored, as they were previously, and old hierarchies are back in place. A Japanese colleague and that colleague when drunk are two entirely separate entities.
Eventually you will become tired of the same old questions about where you're from, whether you can use chopsticks, if it's true what they say about foreigners' packages, etc. It is no surprise so many expatriates end up in a bubble of other foreign friendships. The need to communicate in a language you are comfortable with on a cultural level you're used to is an important one. Instead of shunning the other foreigners for bursting your idyllic "only foreigner in an exotic place" delusion you'll end up banding together for solace, comfort and friendship.
That isn't to say it is impossible to forge meaningful relationships with Japanese people; you will likely make a few good Japanese friends too! Just don't underestimate the social isolation being in a different culture can impose and how other expatriates can help you cope.