Now that the VC exists I think that should be the sole method of re-releasing old games. Remakes like this are often made INSTEAD of new content.
In terms of the 3DS, I'm not really sure what evidence there is to support that claim. While it's true that Nintendo have sought to use remakes like Ocarina of Time and Star Fox 64 to fill out gaps in the release schedule, I don't believe that this has diverted any considerable resources away from the development of new titles. If anything I would argue that utilising remakes in this way (i.e. outsourcing remakes to companies like Grezzo) has allowed Nintendo to maintain some semblance of a release schedule while their development teams pour their efforts into new titles.
The system has been out for less than a year and a half and already we've had Pilotwings Resort, Super Mario 3D Land, Mario 3D Kart, Mario Tennis and Kid Icarus: Uprising. There are also several titles which are currently in the home stretch or are finished and being held for scheduling purposes: games like Fire Emblem: Awakening, Luigi's Mansion: Dark Moon, NSMB 2, Animal Crossing 3D, Paper Mario: Sticker Star. Not only that, but Nintendo have also taken a few noteworthy steps into digital games with titles like Pushmo, Sakura Samurai and Dillons Rolling Western. All the while Nintendo have also confirmed that they're working on a brand new Zelda and Smash Bros for 3DS.
In my opinion it certainly doesn't seem like a handful of remakes, which have been largely outsourced to other companies, have blunted Nintendo's development of new titles. I think the 3DS catalogue thus far proves that it's not necessarilly a zero-sum situtation. If the development of these remakes is handled intelligently it should not make any discernable impact on the development of new titles.
As for people purchasing these remakes and 'ruining it for the rest of us'? These games wouldn't be made at all if 'us' didn't buy them. Personally, I'm an enthusiast of retro games and enjoy experiencing them with graphical and gameplay improvements. One of the most fun experiences I've ever had in gaming was the Metroid Prime Trilogy for example. I also have a new found appreciation for Ocarina of Time having played the 3D edition which took the original and managed to make it look as colourful and pretty as my younger self had imagined it to be.
Do I want Nintendo to release two or three remakes a year? Probably not, but I'm fine with Nintendo selecting a few standout titles for which a 3D remake makes sense and giving them the same care and attention that was extended to those remakes already seen on the 3DS.