TribstyAnn
Me.
Towns Folk
Sega has supported fan games. The result is that the Sonic series, regardless of its critical reception in recent years, is massively successful. Because even kids looking for freeware can find a Sonic fangame and get familiar with him.
Nintendo's cease and desists, on the other hand, have prevented Metroid - your example - from being as ubiquitous. And no, Mario doesn't count, he has an entire console to be the mascot for at his disposal.
I'm not saying it's smart, just that it's their right to do so. Sega can support fan games if it works for them, Nintendo doesn't have to.
Metroid, on the other hand, already has a cult following from older gamers. It doesn't need the help from a bunch of crappy fan games. In the case of AM2R, it was a great game, but directly rivaled their own product. If you were a consumer which would you choose? An amazing game that's free, or good game for $40?