In this case, Nintendo's enemy is someone who took their code and shared it with people, code that was worth about $90 Australian dollars a pop on the American market, without earning Nintendo a cent.
The argument isn't about whether Nintendo lost any money from this happening. They own the code. Period. If you're not happy with what they do with it, if you're not happy with what the game contains, do what other people said. Buy it secondhand. Buy a first-hand copy, then sell it when you finish. Play a friend's copy. Don't play it at all. So long as you traditionally put money forth on Nintendo's products, you've got a voice. If you cease to put money forth, you're using that voice to say so. But saying that this punishment isn't fair, that's ridiculous. Why?
The guy settled out of court. He made Nintendo an offer or Nintendo made him one, but regardless, he chose to take it. He could've gone to court and fought for something different. He could have chosen to make the argument you're making, but he knows it wouldn't hold up in a court. The game is worth it's full value. It sold over ten million copies at it's full value. The marketplace has spoken, and decided it's a fair price.
And then the pirates disagree. Why isn't it fair? Because it didn't cost Nintendo the market value to develop, produce, advertise, and get the game approved and shipped to the various countries? That's true, yes. They're a business, they're in it to make a profit. If they don't, they go under, eventually. The intellectual value is also something you pay for. The people who thought of the enemies, stages, and similar things. Even if it is downright "cheap" to make something like New Super Mario Bros, quite a bit goes into making it the game they want it to be.
And so Nintendo feels their product is worth the value they priced it at in whatever marketplace. There's way to buy it for lower values legally, and some people use those ways. However, to pirate, or to call piracy something that isn't immoral to do, or even to sympathize with someone who pirated and settled out of court, essentially admitting he has no defense for himself, is just a ludicrous thing. He deserved the fine. He decided he deserved the fine. The game is worth market price, and he allowed people to get it for free. Whether they'd get it through other means is irrelevant. Whether they'd buy it or not had piracy not happened is irrelevant. Because of him, however many downloads of his copy got out there are copies that the value of the game wasn't paid for. Plain and simple. It would be one thing if everyone who pirated the game bought a copy at retail, and for those that do, I honestly have no moral problem with that. However, that's not how things happen. Since that's the case, I don't see how anyone aside from a pirate, who steals code, pirates, skimps out on the market price, or however you want to say it, can disagree that he didn't receive a fair punishment.