Okay, this is interesting, but first before all else, you need to have a engine. I'd recommend RPG Maker using the fanmade pokemon engine "Pokemon Essentials" for this type of thing. Using that engine you can import sprites, movesets, and all of that into your game. If you don't have a version of RPG Maker, then you may want to learn how Game Maker works. Games like Undertale have been made in it, and really is not a very complex game programming wise, for the most part.
Here is a link to Pokemon Essentials: https://www.pokecommunity.com/forumdisplay.php?f=244 Because its for RPG maker XP, that is the version you'll need. RPG Maker XP link: http://store.steampowered.com/app/235900/ I'd say using Prototype's stats movesets, etc. for this, by the way.