NES games are stretched horizontally (I assume to 'correct' the aspect ratio), but on such a low resolution display this just ends up making the game blurry and introduces some visual artifacts. I think this is a huge shame, since Gameboy and Gameboy Color games look amazing on the 3DS (with the border) and clearly that particular emulator had some thought put into it (the 3D effect where the screen is slightly behind the bezel is a very nice touch).
If this aspect ratio correction was able to be toggled off, you'd have a very crisp image, as can be seen with '3D Classics' releases of NES games like Kirby and Kid Icarus. This should be an optional setting triggered by holding the start or select buttons during launch, similar to how DS games and GB/GBC games are handled.
I know this will likely never be implemented, but I wanted to make my voice heard. I'd much prefer a slightly unfaithful aspect ratio over the current horizontal blurring. I have some photographs comparing the image on my CRT computer monitor with the 3DS screen if you want those as well. Let me know if this is on the wrong board.