When Worlds Collide
First things first. Pokémon needs to be a MMORPG (massively multiplayer online role playing game). For those unfamiliar with the term, other games in the genre are Star Wars Galaxies, Everquest, and City of Heroes. Basically, you play in a perpetually existing online world populated by hundreds of other human players. Imagine Animal Crossing, but dozens of times larger, and every townsperson is controlled by a human player logged onto the system. (That's another franchise that desperately needs the MMORPG treatment, but that's a different article entirely.)
Why a MMORPG? Think about the Pokémon universe. There isn't a main character. There isn't a grand evil looming somewhere that only you can stop. The universe is full of trainers that are all striving towards an identical goal. "Become the Pokémon master!" You are one of hundreds, likely thousands. The idea behind the Pokémon games has always been that you are competing against those like you, those with the same ambition, to complete your quest. The question becomes, why can't the way you play the game mimic this system? Instead of competing against various trainers that are mere AI constructs, imagine constantly playing against other real-world gamers. No longer are you trying to defeat a trainer that has been programmed to fight, you are facing off against another human being who wants to become the Pokémon master just as much as you do. The very nature of the game universe is mimicked by the way the game is played.
But I probably don't have to explain to you why this system would be incredible, why it would pull you into the game so much more than the current method of doing things. I would imagine that one would be hard-pressed to find a gamer that didn't already believe that a Pokémon game taking place in a fully realized online world would be amazing. There are a couple things to consider before I go all-out with the idea, though. If the game is a MMORPG, you can only play it online. Without an internet connection the world simply wouldn't be accessible. That brings up the fairly realistic problem of audience-limiting. Pokémon games are so popular now that Nintendo probably wouldn't be too keen on the idea of drastically limiting their audience to those with internet connections, and likely even only to those with broadband connections. Nintendo has repeatedly expressed concern about this problem, and it is one of the key reasons they have yet to jump into the online marketplace. By the same token, however, we can assume that if Nintendo is even making an online Pokémon game in the first place, they have found a way around these hurdles. So, for the purposes of this article, let's live in the magical world where Nintendo has produced the brilliant and cheap online service that they have dreamed of.
First, the basics. The game would take place over the entire Pokémon world, not just a single continent. That means you can visit the Kanto, Johto, and Hoenn regions throughout the game, and each region would have different native Pokémon. Not only would this serve to better give the impression that you're playing in a real world, it would create necessary technical divisions. Many MMORPGs mirror the entire world over multiple servers, so there could be multiple versions of the same location with completely different people in each version at the same time. What I'm envisioning, however, is a world where there's only one version of any given place. Everyone is in the same world at the same time. I'll get into that more in a little bit, though, since the initial declaration poses numerous technical hurdles.
Stripping back all extraneous and causational activities, the basic purpose and quest would be similar to all of the previous versions of the game. Start out as a budding Pokémon trainer, acquire badges through battles at against Gym Leaders, and eventually challenge the Elite Four (and the previous champion) so you can be the Pokémon master. I'm imagining a system where all gym leaders are played by Nintendo staff members, who additionally act as server moderators. The pacing of the game would have to be significantly slowed, so you wouldn't be able to rifle through the gyms or max out your Pokémon after a mere week of power-playing. Beating a gym leader would be a significant achievement, not merely a step on the ladder. The game would run on a series of "seasons," with each season having a new champion. The length of these seasons could be as short as a month, or as long as an entire year. I would imagine that the longer the season, the better. After all, if you're trying to mimic the game world you can't rightfully expect to become a Pokémon Master in a mere matter of weeks. However, very long seasons could create harsh imbalances between people who have been playing for months, and those who just picked up the game. For that reason, a middle ground would likely need to be reached.
For balance reasons, there would be a level or ability cap at each gym. Basically, if you already trained a multitude of amazing Pokémon in the first season, you wouldn't be able to use those same Pokémon in the beginning gyms for the next season. You could still use them later on in that season, but you'd have to train some fresh meat for the preliminary rounds. Those who would prefer to continue using their highly trained Pokémon, however, would be able to compete in other organized competitions throughout the season. Numerous clans and teams could be formed around a basic framework provided by Nintendo, so there would be plenty to do if you didn't feel like competing in the standard tournament series. There would also still be the ever-enticing goal of catching 'em all.