Pokemon would have to be rebalanced very drastically if they were to make an MMO.
Before i go on to clarify the above statement, i think your idea of an AR and Street Pass assisted Pokemon game would be dynamite, and could very well be the next big thing the franchise does, and would be a good way to get the kiddies to keep a 3DS in their pocket instead of an iPhone.
But on the above, imagine if Pokemon as it were was made into an MMO, then think of the world of competitive Pokemon and how drastically different it is from the games as we know them. Everything outside the "overused" tier would functionally cease to exist, and then we would have a dry game that would be very, very hostile to both n00bs and casual players very quick.
Given how much they'd have to change about the world of Pokemon to make an MMO work, they might as well just go ahead and make a completely new franchise that works similarly to Pokemon but has different ground rules
Monster Hunter: pissing me off since 2010.
