So I would like to start off by saying that I applaud you guys for switching up the game-play a bit and creating your own world with a Pokemon Theme instead of ripping it out of the Gameboy and calling it a day. I think it will not only make the game more fun, but feel like a legit MMO.
Achievement System
Im sure someone has brought it up by now but I was unable to find it. Personally I feel Achievements should also benefit the player.
Example: Beat all the Gym Leaders = "The Master" = 25% EXP rate increase to all Pokemon
Breed X amount of Pokemon = "Breeder" (sorry for the lack of originality)= Faster Egg Hatch Rates
Beat X amount of Players (who are just as strong as you level wise) = "Blackout/Whiteout" = Earn more Money when Winning Battles
