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Remember that one does not _either_ bring value or cause problems. I expect a typical human being to bring some value and cause some problems at the same time. And you can never measure which one is bigger.
You absolutely can measure the likely degree of problems an immigrant would bring. To an absurd, extreme, example: you have 1 spot open for immigration. Do you offer it to a semiconductor EE with a clean criminal record in his early 30s, or a 68 year old alcoholic high school dropout with multiple violent criminal convictions?
It's relatively easy to design a system that prioritizes skilled, contributory immigration: academic background, professional career, salary, age, ability to speak the host country's language, skills of relevance, health/fitness, etc.
Sure, the EE from my example can snap and commit a crime, or lose his job and get addicted to drugs; but at a population level, it's inarguable that some groups will cost a country and others will benefit a country.
It is mostly propaganda. Said immigrants will likely still never truly socially fit in even with great effort.
The more interesting question to ask is: Why has Japan decided to tighten immigration requirements now? But in my opinion the answer is rather obvious, especially when you consider the current Prime Minister's nationalistic beliefs: It's much easier to blame foreigners for insufficient welfare, ailing infrastructure, etc than to actually improve welfare, infrastructure, etc.
Also, the example of "a 68 year old alcoholic high school dropout with multiple violent criminal convictions" is rather ridiculous. You're arguing a strawman. It's already impossible for such a candidate to immigrate almost anywhere barring some other exceptional circumstances.
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[1] See here, eg, to see how you would fare: https://japanprcalculator.com/
The points-based system is used to allow you to apply for a PR _on an accelerated timeline_; not apply at all.
Having 70/80 points lets you apply for a PR after being a resident for 1/3 years respectively; you can apply without any points after living here for 10 years.
But I will point out that ten years is a major commitment. Surely if someone can hold a job for ten years the default assumption should be that they're contributing to society, not leeching off it.
And no, that 68 year old alcoholic is free to pass into America under Democrat administrations and tens of thousands have. They technically are illegal, but if you selectively enforce immigration laws and offer things like asylum/refugee status without any checks or balances, the net effect is still the same.
Returning to Japan, as the other commenter pointed out, your PhD example is someone that qualifies for expedited permanent residency, a particular subset of migration that Japan has (correctly) decided to encourage.
Japan's culture doesn't take well to immigration, but Canada bars many immigrants or even visitors on the basis of DUIs - I don't have a DUI, and I'd have to jump through many hoops to migrate to Canada regardless, but nobody can earnestly say Canada isn't receiving many, many (too many?) migrants.