For now, IMO, it'll work like Pokemon Conquest, although I don't know how that will change the gameplay as we know it. However, I'm guessing it'll be either a minor thing, so the gameplay is mostly unchanged and trading with past games will be possible, or it'll be a big change and work like Gen III did in regards to trading.
Played: Pokemon Conquest. Progress: Complete Gallery and cleared all Episodes. Playing: Pokemon Black 2. Progress: At the start of the game..