The ability to play as a pokemon.
level them, and learn new moves and everything you usually do for your pokemon, only as the pokemon.
You wouldn't battle trainer battles, there would be no pokemon centers or cities or even many humans for that matter. You would fight other pokemon for territory, for food, fight to defend yourself from other pokemon bigger and badder then you(the games always avoid things like how pokemon would have to eat each other to survive and humans would get their meet from pokemon. tasty.) and might even have to avoid getting captured by the occasional trainer in a super difficult encounter battle.
Imagine going the the different environments that were for the most part procedurally generated and add in specific special areas that would be the same always just in diffrent hidden spots (like the charisific valley or the seafoam islands) that you could discover and set up homes or dens in, and intact(like pokemon Snaps different locals) and interacting and socialing with other pokemon, animal style. You could even lay an egg or something and start a poke-herd! Could discover all manner of ancient pokemon secrets and artifacts (have we forgotten clefairy came from the damn moon?!) and whatnot. Could make pokemon allies that are compatible with your pokemon to fight alongside you and live in your little pokemon community area, so there would still be the pokemon collecting aspect of the game. Imagine a little crater oasis thing in the middle of the world or game map (at a location with some special thing, like a Deku tree thing, or the final level area dungeon you need to spend the game trying to get into) and here all the pokemon you choose to spare instead of eat/kill/"knockout" could then come live in your little community, then you could leave and continue violent battle and survival, but still come back to a safe area to heal.
Could even have pokemon related achievement and item gathering that earned you a collectable item you needed a hundred of or something to get to the final level to beat (like the power-cells in Jak and Daxter)the game at or something. Your could collect different berries or even find pokeballs or special items or plants or items for collecting that would ultimately serve a purpose at the end of your collecting.
You could even have an online mode for battling other players or for letting friends explore your world, finding things that wouldn't be available in their world depending on what version of the game you bought, like the differences between red/blue, gold/silver, ruby/sapphire.
I could go on FOREVER. but wouldn't something like this be great? you could even have multiple character profiles so you could play as other favorite pokemon. i would never stop playing!
That, dear escapists, would be awesome.
EDIT: oh, and as far as gameplay,pokemon battling would be in realtime, no more turn based stuff. that would subtract from the gameplay. You'd have to have strafe buttons so you could remain facing your opponent/opponents (multiple little guys like you would find multiple animals living together in nature, like multiple bellsprouts to cut down without mercy) and different buttons would be allocated to different attacks/affects.
Replace character class and backgrounds with pokemon type and body structure ability,and you have the makings of a great rpg, as you decide where to allocate your exp into which affinities for which moves and abilities.