It's not as if Nintendo is selling systems to certain countries for less because they like those people more or something stupid like that. It all comes down to costs and exchange rates. If shipping is cheaper, tariffs are lower/zero, and the exchange rate is favorable, you'll get the system for less.
If you live in an isolationist country with a weak currency, your system will cost more.
Regional preference may have some impact, as nations like Japan are very competitive when it comes to electronics, so you may have to sell for less to compete with a bajillion other tech-toy options.