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If they just took the handleheld, all all regions and pokemon, limit each server to about 5000-8000 people, and I'd be okay with that.
Except maybe increase the size of things, routes and towns and whatnot.
To keep you from level capping all your 'mons, each region (Kanto and such) you make your characters child, and start the journey again - this will built into the story as well. Always have the option go back and compete in regional leagues.
AND HAVE A QUESTLINE THAT ACTUALLY EXPLAINS BREEDING FOR ONCE FUCK.
Do that and charge 5 buckaroos a month and that's 60 over the course of a year. The same if they release a pokemon game for the DS every year. Sails boosted. Tap the market of 'babby's first MMO,' too.