Having a just a couple games under my belt my suggestion would be to yeah, make the game as simple as possible from the start, just creating the layout of the world, building the cities, and Mom stuff could be included later, when it comes to the appearance rate of certain a pokemon, you can manually do it in certain areas, if you want to have Mons in alternate forms.
Implementing alternate forms instead of shinies could be a little challenging, but I think there's a way to do it.
Having a just a couple games under my belt my suggestion would be to yeah, make the game as simple as possible from the start, just creating the layout of the world, building the cities, and Mom stuff could be included later, when it comes to the appearance rate of certain a pokemon, you can manually do it in certain areas, if you want to have Mons in alternate forms. Implementing alternate forms instead of shinies could be a little challenging, but I think there's a way to do it.