Catch & Evolve got me thinking of a tournament in which players still start with a randomly generated Pokemon but as the tournament progresses they are randomly generated another Pokemon to add to the team, NFEs included, Ubers discluded. If that's not enough of an evolved concept, perhaps something Battle Factory-esque in which three Pokemon are generated (easy with the second generator) and after each battle they can swap a Pokemon out with their opponent's? A clever combination of both in which a randomly generated Pokemon takes the place of one the mons on the team?

Just musing some thoughts/possibilities.