Apparently there's going to be an online storage feature with an annual usage charge.
http://www.pokemonxy.com/en-us/strategy/
"Pokémon Bank is an application and service for Pokémon X and Pokémon Y that will allow you to deposit, store, and manage your Pokémon in private Boxes on the Internet! Pokémon Bank is a paid service, with an annual charge for usage.
Pokémon Bank will be a powerful resource for players who like to obtain many different kinds of Pokémon, or for those who like to raise many Pokémon in preparation for battles and competitions!"
There's also PokeTransfer between XY/BW (the mention of a linked application makes me wonder if one will be able to use it without Pokemon Bank). It won't work with Pokemon that they deem to be created 'illegally'...