I'm in the middle of this debate. I wish Nintendo was more lenient and allowed people to make fan games without shutting them down, but they're not in the wrong for doing so either, since they are their IPs and they have to protect them. So they kind of have to do it. Although I don't believe Nintendo doesn't enable their fans. They do so in other was, such as showing off fan art and being active in the youtube community.
I don't think it's as simple as saying "Sega's good for letting their fans make fan games, while Nintendo is evil for shutting them down!" I'm sure there's more to it than just that.
There's also something to note, despite shutting these games down, games like the Metroid Remake and Pokemon Uranium are finished games, so people can still play them. It's is still sort of a win for both sides. The creators of fan games can still show off their games, and Nintendo does what they need to protect their IPs. It's better than a few games that never even got that far...
Dance my pretties!
The Official Art Thread - The Official Manga Thread - The Official Starbound Thread
