I don't really understand why people get angry with Nintendo for this sort of thing. Other companies LET people mod their shit and use it as their own, they can certainly stop it if they want to as well, they just don't. Nintendo chooses to stop it. Nothing says they should or have to let things like this go.
It's like two apple stands at the market. One of them lets people use their name and apples to put up stands of their own in front of their house, and they don't care if people make money from it. The other stand doesn't like people doing that, they think that if people will be buying their apples, it should be from them, and they should get the profit.
Two different outlooks on business, doesn't mean one is wrong, or one is being more of a dick.