Breaking the 3D rule you set, there is Super Mariomon. It’s a romhack for Pokemon Emerald that does a complete conversion to into a Mario based monster hunting game. The story, the map, the monsters, all 100% replaced. Because it isn’t Pokemon, the creators took some fun liberties on some of the core concepts of Pokemon like gyms. They also masterfully mined Mario lore to fill out a full dex of 151 critters.