When I was in university, one of my favorite areas of study was experimental psychology (physiological being my favorite by a head). One of the things you learned pretty early on about psychological experiments and all surveys, from which a lot of behavioral data is gleaned, is that there is always bias and issues with just how well the data you collect reflects real behavior.
One of the things all foreign people tend to do is reach conclusions about Japan based on our anecdotal experience. We don't do this because we want to offer a skewed viewpoint of life here. We do it because that is what we have access to and it makes a huge impression on us. There is very little you can do about this issue except to seek out other sources of information (which will in turn include their own biases and erroneous conclusions) and, most importantly, be open-minded and flexible in your opinion.
Early on, many foreigners tend to form their viewpoints based on their experiences as English teachers. While conversation school teachers tend to meet a fair variety of people, they are still going to get a pretty narrow view of people in Japan. For one thing, the people you meet in schools usually want to have contact with foreigners and have an interest in expressing themselves in English. You don't meet the average person who has no interest or an active distaste for foreigners very often. Additionally, you tend to meet people who are affluent enough to afford attending such schools and who will tell you things which portray Japanese culture in a favorable light because they want you to like them.
Those who moved on from schools to working in Japanese offices and have direct exposure to the corporate environment have a somewhat broader perspective but it's still far from putting us in a position to understand the culture as well as we might. The types of companies that will employ foreigners tend to need foreign employees for their language skills or they tend to be in the tech industry. There are certain kinds of businesses that we don't get an intimate knowledge of. However, I think you really get a good feel for corporate culture from working in an office and can see beyond the stereotypes of Japanese businesspeople that western news sources offer.
Finally, there are those who marry Japanese people and they probably are in the best position to get a full perspective on the culture. However, even foreigners with Japanese spouses will be treated differently than Japanese people treat each other (and possibly shielded from certain behaviors. Also, some foreigners with Japanese spouses start to form a bias to help them integrate with Japanese culture better. That is, some people will start saying that there is little or not prejudice against foreigners in Japan or start to assert that foreigners deserve poor treatment on the occasions when they experience it because they don't try to fit in hard enough.
In my particular case, I have had the chance to speak to copious numbers of people for short periods of time. In my former job, I spoke to a minimum of 700 different people each year in short conversations. This allowed me to ask a lot of people the same questions. In essence, I have functioned as a one-person surveyor on a limited number of points and my sample size is easily over 10,000. This is a far greater sample than you see in most surveys. Unfortunately, my sample is still pretty skewed as 99% of the people I spoke as a part of my job were male company employees (or college students) and probably 70% were 25 or younger.
In my work outside of that company (at a conversation and as a private teacher), I've had many chances for in-depth conversations with a relatively small sampling of people who are predominately female and over 30. Their responses to questions are vastly different from those that I used to get when I was interviewing young men.
One way in which I attempt to find a little balance for my experiences with other perspectives is to read the surveys on What Japan Thinks. These surveys are also, of course, from limited sample sizes. In fact, most of the time, the samples are insignificant for a population the size of Japan's and the fact that all surveys are done voluntarily further degrades the validity of any survey (in any country, by any method, and on any topic). Only a certain personality type will take the time to answer survey questions. However, at least these samples represent people who are responding in Japanese and are done by a method other than a face-to-face encounter so reading them broadens the range of my perspective a bit more. They're also very interesting as anecdotal information. I often discuss them with my students to see if they concur.
I think it's pretty important to allow your theories about Japan and its people and culture to be open to modification as time goes by. It's also important not to take anything you read on the Internet at face value no matter how knowledgeable the source appears to be. Even after a lot of time and conversations with a lot of people, there are still things I get wrong or don't know.