The new feature in the 3DS store was just announced called Pokemon Bank. Pokemon Bank will allow you to store your Pokemon in 100 boxes online, for 3000 Pokemon in total. You thus store your Pokemon in the cloud and can take them out as needed.
Poke Transporter allows you to upload your Pokemon from Black and White to your Pokemon Bank and then transfer them to X/Y. The games have to be loaded in your 3DS to do the transfer. It's add-on software for the 3DS.
Pokemon Bank is a paid service with an annual fee. It will be a longterm service and will be compatible with future titles.
Also, in X/Y, your Starter Pokemon will be given to you by your friend and then Professor Sycamore will give you either Bulbasaur, Charmander, or Squirtle later on! Venusaur, Charizard, and Blastoise have Mega Evolutions!
It's also revealed that the player's watch combines the feelings of the Trainer with the Pokemon to achieve Mega Evolution.