Let me emphasize this because it's an important point: Nintendo's profit margins are not unheard of. Their profit per employee is historic, but not their profit margins. Nintendo has typically run about 25% profit margins, which is very solid -- about what you'd expect for a company that's run as responsibly and successfully as Nintendo has been. Microsoft (the whole company, not E&D) runs 25-30% margins, for example. Microsoft is also a well run company. There are many companies (including large ones) that run at profit margins of 100% or greater, although few are in the tech field.
What this tells us is that Nintendo's profit margins are perfectly normal and healthy. It does not indicate unfairly greedy or underhanded business practice. What is abnormal, however, are the profoundly low profit margins Microsoft's E&D division has been run at, as well as Sony's Game division: even in their best times, Sony has only managed ~10% profit margins. Those are boom times for Sony Gaming. When they were kings of the market with nearly complete domination, their profit margins reached as high as 12% over any given 3 year period. If you aren't well versed in financial metrics, let me tell you unequivocally: that's not good.
To wit: based on the financial data available to us, it isn't that Nintendo is unreasonably greedy, it's that Sony and Microsoft are unreasonably liberal with their spending. In comparison, Nintendo seems greedy, but what they're doing now is exactly what a responsible and well run company should be doing. However, it's important to remember that Sony and particularly Microsoft don't have to be responsible: they can afford to be grossly generous, and they are doing so. Likely because they believe there is a larger payoff down the road, but whatever they're motivation, that's what they're doing.