The thing is, they are fully aware they will get nothing in return from day one, so this is more of a passion project than anything, "What if Mario had a Portal Gun?" "What if Metroid II had better graphics", "What if there was this new kind of Pok?mon" these games people get passionate about and with the right community they can expand. The problem is that recently, the Metroid remake and Pok?mon Uranium blew up out of proportion, I started to worry when IGN, Gamestop and Kotaku were reporting on it (either that or NX rumors), because hundreds of fan projects have survived over the years for living under the radar, these had sites and millions talking about it, so Nintendo had no option but to do what they must, even if people would get pissed off, which they did.
Also, Nintendo is their biggest targets because their 8-16 bit era games and their Pok?mon ones are the ones that are the easiest to do, but also, the easiest to get assets to, if there was some tool that could ease the edition of 3D (N64-PS1 era) games we would see a lot more of these ones pop up.