It sounds like it's talking about the idea of having an emulator recognize that it's on a 3DS playing a copy of Pokemon Blue for the GB and then running special code that may be built into the emulator to enhance the presentation of Pokemon Blue, perhaps by overlaying 3D models of the attacks during battle.
Sort of like the auto-coloring that the SuperGB and GBC added to games but taken to a much further level.
Not a bad idea to have built in enhancement for popular/'important' games.
(I'm ignoring any 'should this be patentable' issues for the purposes of my post).