We know that the Kami's forms are Exclusive to the 3DS's Dream Radar.
Kyurem is still a mystery as like Deoxys, it can freely change between forms in the Anime. Deoxys was limited to what game you were playing when it was released and given a locational like transformations with the meteorites. Black and White Kyurem's forms are similar to Deoxys, so they may have a location transformation for it.
As for Key Items changing, that wouldn't effect compatibility as Key Items cannot be traded and therefore wouldn't effect how the game interacts with an older game.