The fact that it's on the DS shows that intercompatibility, perhaps akin to GSC to RGBY, is more than likely here. We've got examples in HGSS of certain Pokémon and items not being tradeable so the system is there to do it.
It won't be a "reboot"
I am of the mindset that one new aspect of the 5th gen games will be genetic variations. As the Pokémon take the lowest evolved form of the mother, the father's genetics are just utilised for attacks. However, what if they now include aspects of the father. So species from the mother and various genetic traits from the father.
This is my theory for why this Pokémon exists in HGSS, as a preview for 5th gen;
This would definitely be a franchise reinvigorating feature