Suggestion number one : " Two man party battles "
Enter a dungeon through a queue, then battle a couple of trainers until we reach an extremly hard legendary pokemon, it will not be catchable.
Beating it will yield experiance, items and other ingame awards.
Two pokemons per player
Difficulty will be mathmatically processed according to the pokemon levels.
Suggestion number two : " Change the name of the game, change the spirits, sounds "stop using anything from nintendo, make the community contribute and pick what you see fit, then release a better game, "you can look at world of warcraft as an example"
This game has infinit ammount of potential this way with a better engine you can implement a lot of different things and the players will not mind a subscription/one time fee+ donations.