For as much as I agree with the overall sentiment that the 3DS VC can be 'both', I have to side with azeke and pokepal148 on this one.
As someone who owns an embarrasing amount of Wii VC games I find it quite disheartening when NES games are released on 3DS VC. First off, my stance on what a license to digital content should constitute puts me at odds with rebuying games I already own digitally on other Nintendo platforms. Secondly, as pokepal148 alludes, Nintendo have a zero-sum mentality when it comes to downloadable games. In other words, when a NES game is released on 3DS VC it will often mean that another game is not. Given that I already own a digital license for all those NES games released so far on the 3DS, if they're not going to give me access to them on the 3DS then I'd much prefer they just release more handheld VC titles as those are games I don't already own digitally.
I agree that theoretically 'There's no reason it can't be both', but the history of the VC service is proof that Nintendo don't curate releases in a rational manner.