New updates and patches are now available for all the Pokemon games on the 3DS. This includes Pokemon X and Y, and Pokemon OmegaRuby and AlphaSapphire.
The patches do not bring with them any major gameplay change or even a visible bug fix- it’s mostly behind the scenes tinkering and some stability work. It can also be assumed that the updates address the multiple new exploits that have begun to crop up in the games that permit players to hack, duplicate, or generate Pokemon illegally, and obtain them without actually encountering or acquiring them in game.
To enforce the new update, it will be needed to play either of the games online any more. it won’t take too much space on your system (or indeed, too much time to download). However, it is a mandatory patch required if you want to take your game online.
Pokemon X/Y and Pokemon OmegaRuby/AlphaSapphire are both available exclusively on the Nintendo 3DS.