I would probably make my very own region and stuff. I would try to make it not campy like the real games and not EXTREMELY HARDCORE like reborn (feels, so many feels). Sue me for this, but I would mix in some fakemon in it as well. Pokemon has so many different outlets for their designs and some are based on inanimate objects, so why not. As for the region, I'm thinking fantasy medieval with a touch of steampunk i.e. Halls Moving Castle and the like (apologize if it's not steampunk, but what do you call those weird flying things the army uses in the movie?) The reason for travel and the gyms and elite four could be replaced with a squire to knight to general type tale where instead of gym badges, you get ceremonial daggers as key items that can be equipped to pokemon for special abilities. Personal favorite idea, follower system. Let say half way through the game you meet token side-kick and they want to follow you in your adventures like Brock and Misty, then they follow you and do special things like being a HM person or maybe a mobile PC for pokemon boxes (I would nerf it by having only one follower at a time). Not to mention now every battle you have that isn't scripted as a single is now a double battle. I want the starter city/village to become like a secret base in other games were as you progress you gain more prestige for the town which makes it better to the point where you could theoretically get ultra balls there, while great balls everywhere else. Lastly bad guys, the kingdom is under threat by three major forces, Devote of a false god (Helix protect us), Barbarians from another region and/or nearby islands, and Dragons. Dragon Type pokemon will be antagonists in the game and are thus uncatchable, side for a select few and this does not count post game (go nuts dragon catchers). This is only a rough idea for it, but i think it make a pretty interesting game. I would put choices in this, but then you have to think about each and every choice and what would that entail, so I'll leave that out of this.
EDIT:
Forgot to say this while putting game system here. The name would be Pokemon Royal Onyx (Not the pokemon, the gem stone), there would be hopefully 100 fakemon, give or take, and it would be from 1 as in a "pokemon game(fake)" to 5 as in "Reborn Nuzlocke", I would give it a 3 maybe 4