Super Princess Peach wasn't an established franchise, and it did well, didn't it?
And I kinda disagree, because it is an established franchise that appeared on both the NES and the original Gameboy. I don't know how many people owned or played it back then, but odds are many of them would pick up a 2D remake just for retro sake, and even Nintendo fans like myself who never played it would consider picking it up to see what all the fuss was about.
Plus the beauty of a 2D version is it is much cheaper to develop, so even if it doesn't sell quite as much, it could still be just as profitable as a 3D version. And like I said, Nintendo could make both and then we all could see how great they do in comparison... and they'd probably mutually promote each other, because chances are someone would get at least one, and then if they are amazed by it they could consider the other as well.