I know the 3DS apps can link to DS games, but I'm not sure that 3DS games can link to DS games, besides, PMD3D didn't have enough memory space to have all 648 pokémon in 3D models, so only around 160 Pokémon appear in it.
So I don't think XY will have enough for 800+ Pokémon. Thus some pokemon might not make the cut. So, some Pokémon might not be able to be ported over, causing problems as well.