Pokemon would be served much, much better by an MMO setting. Half the fun of the series is tweaking your team into a well-coordinated platoon of brightly-colored murderers, and then making small children cry. To be short, the multiplayer aspect. Having a large and, most importantly, accessible community would not only permit the gameplay to transcend, but would likely be the most profitable decision Nintendo ever made.
Pokemon already moves a ridiculous amount of merchandise - add the inherent addiction factor of an online game, and your fans would never stop paying. Or, if you're feeling more subtly evil, make the game free but require microtransactions to acquire favored pokemon, costume options, pokemon customization options (blue charizard? with a cubone hat?!) and battle items. Guilds could be retooled as unofficial gyms, complete with practice area and the ability to challenge rival gyms to tournaments. Scale it so that you don't NEED pay pokemon to be competitive, as that's a quick way to doom your soul to eternal torment in a cyber-hell of my own twisted design, but make it an option for people who absolutely NEED an umbreon. With a pink bow. To feel complete.
I think I may just have invented crack.
