Added, and do you mean the ORAS pokedex ?
When ORAS links with XY, new Items and moves that was not available in XY are not usable by the ORAS player. so if i have a team with Mega beedrill, i cant use the beedrill megastone. (but i am not too sure if it means i can still battle but just cant mega, or if i need to remove the item before i can use beedrill.) i do know if you attempt to link with someone it warns you that they are using XY before proceeding.
Also I got my team finished last night and was doing some test battles on battle spot. it was actually planned for doubles this time, and not just my singles pokemon mashed into a doubles team.