You'll have to wait over a month to transfer old Pokemon
While you're running out to get your Shiny Giratina to transfer into Pokemon X and Y, you won't be able to actually perform said transfer until December 27th. For those of you who are unaware, Nintendo is running things differently this generation. Previously, most new Pokemon games had some sort of in-game method of transferring in old party members -- but it required two portables, two copies of the game, and it was usually pretty cumbersome and time consuming (plus, at least one game made you beat the entire story before transferring anything).
The new Pokemon Bank and Poke Transporter App will alleviate a lot of those concerns by making transfers available right away (when you pick up your Pokedex relatively early in the game) with a much efficient interface to boot, but you'll have to wait a little longer to take advantage of it, and you'll have to pay $4.99 a year to use it once you've exhausted your 30 day trial.
Beyond that, there are a few concerns Nintendo will acknowledge "closer to the launch of the App," like hacking concerns, and what happens if your Pokemon are stuck in online limbo after your subscription is cancelled. I'll be using the App myself at launch to transfer around 500 Pokemon to X and Y, so stay tuned for some impressions from one of us down the line!
Nintendo of America [Twitter]