I was in the minority when I expressed this opinion, but I don't think this is a Virtual Console. There would be far more effort converting games to 3D then there is customizing the emulator and packing up existing rom files. Nintendo would either have to charge more of the titles (and risk cutting off impulse buys) or accept lower margins on VC 3DS.
I think it more likely that this game is presented like they plan to sell it, as part of a block they can charge more per game for.