Hmm, never put to much thought into it myself, but my own Pokémon game would kind of be a cross between PMD and the original series. Not sure how that would work out exactly, but I would think in battles, it would have to be like Final Fantasy with the Real-Time Battle Mechanics. I'd say it would be on two consoles, the Wii and DS.
What I mean by a cross between PMD and the series that started it all is this: You as a human, come across three mysterious stones with the Professor of some region. You and him are attacked suddenly by a gang of crooks wanting them for themselves. You decide to pick one up as the stones are deemed as important, and upon touching either one, your body shapeshifts into one of a Pkmn Starter. You then take out the crooks singlehandedly in an RTS Battle, and shapeshift back.
The Professor then realizes the stones' potential, and decides to take the rest with him while leaving the one you grabbed with you. He then decides on giving you a Pokémon Partner to travel with you to keep you company and grow into friends.
There would even be an option to change your attire slightly. Adding and removing armor, accessories, etc would influence your character's and partners' appearances like in the Elder Scrolls, all while affecting your stats.
When going online with Wi-Fi, you could chat with others, battle them, and even trade items. Also while online, you would be able help others in missions simultaneously, all while advancing the story.
After beating the main story, there would be some special sidequests you could do, including going into a distorted reality that decides to threaten your world, and stopping it from spreading.