There are plenty of ways to chansey this good idea MMO up. This is a MMO and not a Classical turn based pokemon game (It needs to be a perfectly well tuned STRATEGY game that always will have good TRAINERS thinking about perfect party combination with right abilitys for each occasion). I have seen a lot of little kids post in the forums with stupid ass retarded ideas that would chanseyed up a MMO but maybe not their little old school classical type pokemon game.

What would be a game-breaker would be players able to use Legendary pokemon, what i have done in past games was grab all the legendarys and blow stuff up with them, i really never felt the urge to play with any other pokemon because i had the legendarys.
These legendary pokemon should be 'bosses' in the game, just uttering the words legendary pokemon should strike fear into all players. These Legendary pokemon should be in their dwellings protecting their caves or what ever they live in, it should be a goal to navigate through the cave, fighting difficult pokemon to get to the end where the legendary pokemon will be sitting there waiting for you. Once engaged it should take your entire party of pokemon to defeat him, and a reward would be given to you once its done and thats up to the designers to figure out.
There should be time to set up a perfect party to navigate the cave and to defeat the boss.
(rewards could be, rare candy??, stones  (make stones really really rare other than boss fights) poke balls, Rare boss ablilitys from a TM)

I hope this game is more strategy involved instead of just trying to kill everything with your starter pokemon like i normally do in the other games and it works too good (except on some occasions where i mite get another pokemon that can do it better but only on a rare occasion).

I have more ideas and i will post them if i get good feedback from developers such as ideas for zones and caves, Gyms and all sorts of stuff.