In the case of Pokémon XY, 3D isn't a new thing anymore, it negatively affected roster size and all the other factors that also contributed to PS era boosts are missing as well. 3DS is more comparable to PS2 and SFC than to FC and PS. The follow up gen to a huge platform often has better libraries in terms of core content but with less of the casual audience than before, the biggest franchises suffer. Pokémon is big enough to be affected by that lost audience, just less than a more casual heavy franchise like Layton was.