The reasons for it may be few, but the reasons against it are none.
There are literally no good reasons to be against MM3D besides "I don't want it to be remade". As I stated already, making it will earn Nintendo money, let people have a mobile version of Majora's Mask, show the game to modern...
I am all for Operation Moonfall, there is no good reason to be against it besides personal opinion, no one has actually stated any factual reasons for Nintendo not to make it.
I can think of a few really good reasons to be for Operation MoonFall; it will bring one of the best Zelda games ever...