While this would most likely never happen, what if in future generations instead of placing Contests or whatever in the game, GameFreak opted to include several cards from the TCG that you could find around the field or even purchase with in-game currency? Then, you could go to certain halls and duel with people there in different tiers (the same way a contest would work).
I don't know, I always thought this could be a cool idea, and I loved when Final Fantasy VIII did it. I realize that this would take away from the online TCG, but a man can dream. --- "Embrace your dreams" - Zack Fair, Crisis Core 3DS Friend Code - 3222 - 5572 - 0469