The high percentage options are a) spouse of Japanese national, b) engineering status of residence (need to be able to demonstrate approximately ~3 million yen a year in income and an ongoing contract with one or more Japanese companies, and it is highly to your advantage if they're established old-line companies), and possibly, c) intra-company transfers (easiest to accomplish for established startups with significant ex-Japan operations), and possibly d) the new point-based immigration system.
(btw will be back in Tokyo in September, would love to buy you coffee)
I haven't actually read the fine article yet, but I'm not really sure what would attract people to doing start ups in Japan. Hiring locals is difficult because of the way the job system works -- people don't change jobs every few years. It's quite a bit cheaper to live here than many other places in the world, but it is culturally very different. I spent 5 years here teaching English amongst many young (mostly American) colleagues. I wouldn't bring people over here unless you are prepared to help them out a lot when they inevitably get in trouble (shuddering recalling the experience of having to help my colleague who punched a police officer). It's a big commitment. Also, unless you have a lot of experience with Japanese culture yourself, it can be a bit tricky to handle all of the business issues. For my business, I write code and leave all the business issue to my Japanese wife (even though I am quite fluent in Japanese). Without her and my accountant, I would be lost.
But, of course, Japan is an amazing place if you are the kind of person who fits in here. I wouldn't want to live anywhere else.
From what I know, it sounds like it is relatively simple to hire someone with college degrees, as long as receiving company can demonstrate they will be able to support (e.g. Company's big enough, making profit, etc.), but having even one factor outside of these parameters can severely make this complicated or impossible.
Does that mean it's easier to bring foreign hires into Japan, or into US?
But you need to find a company that is willing to sponsor you, and speaking Japanese is a requirement for most of them. I mean if is not impossible to find a tech job where only English is required, but you will have to compete with a lot of other candidates from different nationalities; whereas if you are bilingual and you have an acceptable CV, finding a job is extremely easy. In some cases, maybe even easier than for a Japanese who is monolingual.