I think it is time for a WoW-style Pokemon MMORPG

With every region and every Pokemon available from the start. Ability to challenge gym leaders and collect badges for entry into Leagues, with the leagues set up like the TV show(i.e., if you get your 8th badge, you reserve a slot in the next Indigo League tournament, a new one will start every time there are 256 eligible members). Ability to challenge other users. Turn based battles(like the games). All gyms would have multiple gym leaders, so you are always facing a real person and not an NPC. Ability to form traveling parties, including the ability to align yourself with factions like Team Rocket. Or you could go another route, like just being a breeder, competing in Competitions, etc. And of course, the old standby-a roving Magikarp salesman. The only player vs computer battles would be against wild Pokemon.