Yes, I do realise that this has been posted so far, but I haven't read one in a long time, and I'm hoping some Nintendo scout is reading this, lol!
Anyways, how about if they connected every pokemon region together, and they putted every pokemon in the game out there.
The battle system would work like WoW, there won't be a ''You attack, my turn, now your turn etc etc''. When you encounter a wild Pokemon, you are getting the option to pick one of your three pokemons currently on the team. (I know the usual deal is 6 at your team, but I think that this would make it an everlasting match against a player, so 3 is fine).
^ When you have chosen a Pokemon to battle with, you will be that Pokemon, take for example in WoW, you controll a character. you will control your Pikachu like you control your normal character. So it's all about skill to win! Wouldn't that be fun?
You would also only be able to exchange pokemons during a battle every 4 min.
It will be a beautiful MMO World, take the graphics from Naruto Ninja Storm 2 or something and imagine that.
Legendary pokemon will NOT be capturable, but a rare sight, a very very rare sight. Arceus may pop infront of your face, or it may never do so.
The game would also include dungeons, for example a haunted house with Haunters, Gengars, Banetta, Dusclops etc etc. They would be really powerfull and your team would have to use your skillz to manage to down them.
The game would NOT, NOT NOT NOT NOT use the ''Holy Trinity'' system; Dps, Tank, Healer. It would be based on your skill, to dodge, avoid and counter attacks.
What do you think of this? Sorry for grammar erros, I'm not from an english speaking country!