Spore/Civilization.
Start with controlling Mew and gather mythical powers from finding special areas still affected by the strange powers of creation (Arceus and the likes) to get new powers, and eventually mutate into another species. Then control a herd / family of your species to become more refined. Maybe fossil pokémon could be used in this stage and eventually evolve into non-fossil types. After that, play a tribal war to conquer other species and assimilate them into your civilization, so that you no longer control a single species. And after that, build cities and create traditions and tournament systems and whatnot. There could be both a RTS-like war system and a "peaceful" pokémon league system with regular pokémon battles.
I'm thinking of a world without humans, here, more PMD style but probably more advanced at later ages. With plenty of multiplayer capabilities for warring, tournaments and cooperating. Epic.
@ Brendino, I thought about superheroes too! But there is that already ;) Pokémon RéBURST kind of makes humans superheroes when merging with pokémon, and there is Phantom Pokémon 7 or whatsitscalled, a manga about a Lucario and his human friend who is a sort of thief/hero.
But yeah, a proper Marvel x Pokémon crossover in some format would be cool. Not really seeing how it would be done though. Maybe by letting pokémon take over the roles of fitting superheroes xD Zangoose = Wolverine?