Hmmm, just like Yu Gi Oh is well the only way to make a story based of Pokemon TCG,more interesting. In reality, in my opinion, its bores me to death when it comes to TCG. Until something exciting happens. But if you want to do a Yu Gi Oh style to it throw in some flavor like idk, implement Beyblades (bit pieces) or Bakugans or something, Chaotic (you turn into a Pokemon, in a virtual world)
You can also have the story take place in the real world , but in the gaming world, its a whole other world like Chaotic, Bakugan, Digimon, Metabots, Monster Ranchers. Or Cardcaptors...well its complicated to explain and its a really old anime, that I don't think anyone even remembers.