Touche, never thought of it that way. Now that I think about it, those SNES, NES, GbA, DS etc injects are effective because of the use of the gamepad alone, which means portability. I just hate having them cluttered in my list of Wii U games in Loadiine. I personally name all my Virtual Console games with z, example: zSuper Mario 64. This way, they always appear at the end of the list all together. Or you can name it: z(N64) Super Mario 64, then all your N64 games will be together, AND at the end of the list.
But yeah you made a good point, that gamepad would be awesome to play on for these games. For me personally though, anything under the N64 can easily be played on my 3DS.