Pokemon should serve a function beyond simply battling. One of the major things illustrated in the show is that various pokemon can be used to solve various problems. Simple examples would be the use of Rock Smash to clear a path or surf to travel over water.
Also, since the pokemon world is very clearly huge a great Pokemon should also offer an alternative means of travel, assuming they are the right size. So instead of wasting money on the bike maybe you have a Rapidash and you ride that, or a charizard to fly you around. Of course to balance this against actually buying the bike, maybe a pokemon has a riding stamina so after awhile they need to be put back in their ball.
Another point to look at, that pertains to combat would be controlling the pokemon. I think that once a pokemon is brought out the player character assumes control of the pokemon, while their avatar follows. A pokemon should have two modes, combat and exploration. The combat mode limits the pokemons walking distance (sort of an invisible wall that keeps them close to their trainner) at this point the trainner stops moving allowing players to focus more on the battle and less on wondering into angry, wild pokemon. A side from a change in mobility combat and exploration mode could have a difference in use of a pokemons abilities. So while in combat mode rock throw plays out an animation of your pokemon picking up a rock that is not persistant to the world ( you don't need real rocks to be around to use the attack) the ground and throwing it, in exploration mode the pokemon picks up movable rocks in the world and places them where ever the player so chooses. This allows for problem solving on another level within the world itself and allows for some fairly creative puzzles.
Oh yeah, combat should require real player accuracy rather then relying on a stat. This allows for strategy as well as use of terrain in battle.

I thought that it would be king of fun if there where seasons on this game(fall,winter,summer and spring). Just like in the real world fall and winter would be the couldest parts of the season it would rain and snow would be all over. Spring and summer it would be warm and hot the sun would be shining more. What I'm trying to say is bring more of a real world kind on affect in the game.

I think that the user's of this game should be able to have emphasis on what they want to become.I think that it will make the game stand out more than any other mmorpg not just a pokemon game.
What I mean is less emphasis on becoming a pokemon master and more on what the user wants,such as being a Pokemon Trainer,Breeder,Coordinator,Item creator/seller,among other possiblilities. Maybe even opening your own gym?

The thing that can make this game better than the DS game is trading. In the GBA and DS game you can only trade pokemon with other people that have the same game on the same handheld. Trading on this game you should be able to trade buy just requesting trades with other users make it a very easy and simple thing to do. Also the should be a trade balancing system where users can make a three or more user trade.