A 3-D Pokémon game with all the Pokémon and all five the regions would just take up too much memory. Pokémon XD and Colloseum already take up 45+ blocks and people complain that they are too small.
The perfect Pokémon game would indeed be a MMORPG. Here's how I would like it:
-It would be in 3-D.
-The setting is in Johto, complete with the Day/Night feature. Just imageon looking at one of the towers in 3-D or looking down from the Tin Tower across Johto during a sunset.
-There should be no wild Pokémon. First of all, they would take up too much memory. Second of all, the game should be all about the scenery and trainer battles. Third of all, especially legendaries wouldn't work.
-To make sure that every trainer looks different, you get to design your own character in a simular way as in The Sims 2.
-Since there aren't any wild Pokémon there, you will have to upload your team from the GBA/DS or transfer them from your XD/Colloseum memory card. For the people without another Pokémon game, you can rent Pokémon at Earl's Pokémon Academy. But they are just like the Pokémon in Stadium (2), they have their EVs evenly spread out across all the stats and you can't choose their attacks.
-You can both battle another trainer or trade with another trainer. You will not gain experience by battling.
-Once every week, there will be a tournament. The winner gets to choose one Pokémon of choise. This includes Mew, Celebi, Jirachi, Deoxys, Ho-oh and Lugia. If you choose Lati@s, they will hold a Soul Dew, every other obtainable legendary would hold a Sacred Ash and every non-legendary Pokémon would be shiny and would hold a Leftovers.
-The tournaments will be held at different locations each time, like at Whirl Islands, Mount Silver, Nation Park or even something like Slowpoke Well. Depending on the location, there will be different rules. Like at Goldenrod, there will be a tournament for lvl 5 Pokémon (Little Cup, anyone?).
-Everybody participating in the tournaments will win a prize, varying from an Oran Berry to a Lucky Egg to TMs depending on where you ended.
-You get points for every trainer that you beat and you can exchange those points for the same things as in the Battle Frontier.
-Once every few months, a computer controlled Team Rocket could appear that everybody then has to defeat.