It would be set in the late middle ages, and take on a darker tone than the series. War and violence, but excesses (gore, rape, horrible execution methods) would at most be hinted at to keep it from being too edgy.
Pokémon here will be depicted more as wildlife, as forces of nature, and weaponised as elements of human armies.
The protagonist will wield a weapon himself, and can fight Pokémon by himself (which will work fine for low-level critters, but don't expect to be able to take down, say, a Tyranitar). To really get ahead, you need to befriend Pokémon though, and have them fight for you.
With hand-made Pokéballs being prohibitively expensive, after proving your (parters') strength, you'll have to win a wild Pokémon's trust by levelling up your player character's charisma stat through interactions with NPCs and sidequests before it entrusts itself to you.
Besides feral Pokémon, you will also face bandits, occultists, and later in the game enemy soldiers and knights; some relying on weaponry, others on their Pokémon's powers, just like you.
Pokémon Centers aren't a thing yet. Going Nutzlocke would be too harsh, but if you don't level up your alchemy and herbalism skills to make potions for them, their health after being fainted will only recover gradually; and if you make them fight while they are in this weakened state, they might actually die.
The plot will be kept simple, and the world relatively small. Two or three villages, a larger city, a few castles—and much nature in between. Forests, mountains, meadows, where many wild Pokémon dwell. The emphasis is on you and your Pokémon exploring a dangerous and untamed world—braving dangers, growing stronger, and in the end proving yourself a worthy vassal to your liege on the battlefield.
