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.
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.
---
[1] See here, eg, to see how you would fare: https://japanprcalculator.com/