I'm curious what problems you've seen with the Japanese immigration system. Every time I've had to do anything it's been literally a rubber stamp type affair. I admit to not having to deal with any grey areas, though. I've always obviously fit the criteria for the visa.

Here's an example I ran into - the Highly Skilled Professional visa has a hidden requirement of being eligible for one of the other visas, first. This requirement is only expressed (as far as I know) in internal memos given to the immigration offices and not posted anywhere in the English language internet. So, if you don't have a degree, you can be eligible at first glance for an HSP visa (due to a combination of age and countable years worked) but ineligible to actually get it, due to not having 10 years of countable experience.

Edit: It's also not clear at first glance what counts as "work experience" - if you have first and last paycheck + contract it's easy, but if you don't it's fuzzy. Open source or hobby programming is no good.

In general I think the system is rather good. If you have a job lined up getting into the country is pretty smooth and renewals are mostly straightforward.

Probably the most common source of problems I see is the rule that you must have a longer than 1-year residence status to apply for permanent residence. The max I've seen is 11 one year renewals in a row. It really does seem random. One situation featured a couple were both employed by the same company doing the same job, came to Japan together (same entry date), were living together (same home address) and yet got different lengths of residency.

I think it's clear that an opaque system is a feature not a bug as far as the immigration office is concerned, but that does little to put the minds of people stuck in the system at ease.