I've been playing other MMOs for the last 5 or so years, mainly FFXI but a good dose of WoW, City of Heroes and a few others thrown in the mix there. Pokemon doesn't need to be the next World of Warcraft, in fact I don't think it should be, but there are certain changes that would need to take place if the franchise wants a fun, successful entry into the MMO scene.
Here are some ideas that I've been mulling over for a while now. I'm not sure how feasible they all are, but you've gotta start somewhere right? (Since this list comes from a text file where I've just been adding idea as I think about them, it's a bit sloppy. Some things may be repeated or worded awkwardly. I apologize in advance.)
* All regions - Johto, Kanto, Hoenn, Shinnoh, Orre, Fiore - including the variety of gaming flavors found in each. (Want to participate in Super Contests? Gotta go to Shinnoh.)
* Having the Underground make a return
* User-made content (trainer appearance, secret bases, personal rooms, etc)
* Crafting system (custom made pokeballs maybe? Seals, ribbons?)
* Different Classes (Trainers, Breeders, Coordinators etc) - Don't want to spend your days and nights simply battling other pokemon? Then perhaps you can be a breeder or a contest goer? Maybe even set up a shop or a wilderness Pokecenter for your other trainers! Farmers = specializing in berries, growing stuff, pokemon herds for crafting materials, quest-related items?
Trainers the general basic job. Goal: Complete the pokedex
Breeders have access to the regional starters, reduced egg-producing time. To "stay" a breeder, you may have to breed a starter for the local pokemon gym.
Rangers - trades the ability to permanently capture a pokemon to be able to freely set up a wilderness Pokecenter for trainers (other classes have to pay in $ and materials)
Coordinators - slightly weakens pokemons' battle power in exchange for increased "Trainer stats" or something
Merchants - Earn more $ from battling trainers, can set up more than a single shop
(More trainer ideas? Professors etc?)
* Make getting legendary pokemon DIFFICULT, needing teams or groups of people working at the same time, though only one will get the pokemon at the end.
* Quests - rewards could be currency, pokemon, "reputation" etc
* Protection against cheating
* Minigames
* Events - seasonal, official Nintendo events!
* Pokemon are given a lot more variety in catching.
* Time based events would have to be worked out differently. A world wide release would be difficult if game time = real time, unless each Region were large enough to encompass various time zones, ie Day in Kanto could mean Night in Fiore
* Trainer levels, "stats" - independent of pokemon stats
* There'd probably need to be a limit on how many pokemon a train can "own" at a given time. I don't think a server could hold 10k players each having over thousand pokemon stored somewhere.
* "Favored" Pokemon system - think Pokemon Yellow's Pikachu, just with any pokemon of your choosing, they get bonuses to their stats, and stay out of their pokeball
* Livable space - for a cost players can buy their own bedroom/apartment (otherwise they have to logout in a POkecenter or some other safe spot to avoid losing a random item, exp, money or something...) Also provides item storage.
(Or perhaps, like the Machoke guy in the Gen 1 games, players can buy land and build their houses from scratch?) Keeping everying pokemon centered, they'd have to hunt down building materials or fight a Zoning Director in a "gym leader"-like battle.
* Players can have a bedroom/apartment, a secret base or an Underground base - perhaps all three after fulfilling the right quests. Can be decorated. May provide instant transportation between the three. (Have a bedroom in Kanto, a secret base in Orre and an Underground base in Hoenn)
* Pokemon Releasing system - Releasing a pokemon makes it live in general area for a period of time (different for each pokemon). If enough of the same sort of pokemon are released in the area, they could become part of the local environment - perhaps even spawn quests if they are deemed to upset the balance
* Random and non-random encounters
* With enough real estate, players could possibly start their own small towns. (Chansey-burg! Pikaville!)
* I'm not sure about 3D gameplay, but I'll include it here.
* Some sort of in game economy to spur on player/player interactions. Sorry folks but the stuff that's typically free will probably need some sort of cost associated with it when shifted to an online context - Pokecenters, accessories, etc
* Players can form Groups (a la DP) which can grow into "unofficial" but League sanctioned Gyms.
* A game flavorful and casual enough for folks who can't invest mega hours into the grind, but can be robust enough for folks who do want to
* PvP - special arenas, a Pokemon League
* PvE - imagine fighting against Lawrence III and his mind-controlled Legendary Birds in a revisioning of the first Pokemon Movie.
* Pokemon swarms, of course
* Shadow Pokemon break outs - perhaps if there's a "world-wide" lake of caring for one's pokemon (or maybe just because Cipher is up to no good) Players may find that a pokemon or two has somehow closed it's heart off. It's more powerful in battle, but can't do a field move, or collect material or help with crafting etc.
* Wii and PC versions, possibly
* Some revamping of Pokemon movesets, battle mechanics...
* Perhaps a DS game that allows some limited leveling of an online pokemon offline (though not in a DS game setting)
* Voice chat or some sort of communication that's more robust than preset phrases
* Upgradability - New pokemon generation? New expansion or (free?) downloadable content for the game.
* Twice a week DS (or Wii?) to MMO transfer - cheat protection though! Trying to transfer a Master ball or the like would net you a berry or a "No Cheating" mail instead.
* Someway to keep the handheld games popular enough where Nintedo would actually say "Yes" to a Pokemon MMO
* Some business model that works, but won't hardship one player over another. Monthly fee? Completely free? Free with a cash-shop?