It sucks to hear you've been getting one year renewals. Unfortunately when it comes to bureaucracy here in Japan, things are on a case by case basis, so its hard to make any sweeping judgements. As a counterpoint, I came here on a working holiday visa (6 months) and found a job at a Japanese startup. When I renewed my visa, I switched to an Engineer visa and got a three year one.

Mid-way through that three year visa, I quit, and created a consulting company. After consulting with an immigration lawyer, I was told it was "probably ok" to be the director of a company on an Engineering visa, so long as the primary thing I was doing was Engineering related. When my three year visa expired, I successfully had my own company sponsor it, and got another three year one, followed by a five year one. Last year, I successfully got PR here.

Its hard to say why you're continually getting one year visa renewals. If you're not already doing it, it could be worth having an immigration lawyer submit the application on your behalf. Because it was a cheap business expense (~80,000 JPY) compared to the cost of screwing something minor up, that's what I did for every renewal I did under my own company (for PR, I did it myself though).

I'd argue that Japan has a relatively friendly policy for skilled immigrants. To get a job as a developer here, all you need is a company that's willing to sponsor your visa and a university degree in a related field. As far as I'm aware, there's no onus on the company to prove they couldn't get a Japanese to fill the position, or quotas on the number of visas like there are in other countries (US for instance).

Furthermore, a great thing about Japanese working visas are that they aren't tied to a specific company, only the field of work (which they've made broader by combining several statuses into the Engineer/Specialist in Humanities/International Services visa category). This means once you have a visa here, you can easily switch jobs, and even if your company was to lay you off or you were to quit, you don't immediately need to return to your country.

What's more, Japan's introduced a points based system to give preferential treatment to highly skilled professionals. While the points they give create a bias towards someone coming from academia or working at a large well paying job, it makes it theoretically possible to get PR here without being married to a Japanese citizen after one year.

There are a lot of problems with Japan. I agree with you that the trainee visa is one big one. The lack of being able to get a clear answer about immigration status issues also makes it challenging, and encourages you to take a certain amount of risk in stepping into a grey area legally, which I understand will hold some people back. But for me personally, and other foreign entrepreneurs around me, it has made it possible to transition from being an employee to entrepreneur with relatively little investment compared to what is required in other countries.

If anyone is interested in more detail about transitioning from an engineer to entrepreneur here, I've written more about my experience here: http://www.tokyodev.com/2014/04/17/creating-company-japan/.