It all depends upon the setting of the fic. Since Johto and Kanto are on mainland Japan, they share many similar pokemon. However, Hoenn and Sinnoh only share the most common of the mainland pokemon. My fanfic is set in Hakkou, a region to the south of Japan (think Taiwan but scaled up and moved a bit east) and has many new pokemon - over 300. Why? Its a sub-continent that hasn't had contact with other places geographically for a long time. It is massive, having its own mountains, volcanoes, and even a recently recovering portion of dinosaurs. This is because, like Australia, it has not been connected with main species of common pokemon.
Take for example, Charolt. It is closely related to Ponyta, as well as the mainland equivalent which became extinct a long time ago. Charolt, instead of remaining a pure fire type, for some reason evolved (in the Darwinian sense) to incorporate the dark element. The Ponyta and Rapidash retained their monoelemental status, and thus have different coloring and elementage than Charolt. The same could be said with the mainland equivalent.
This above property can be applied to nearly every situation. Dwarfism would dictate on islands such as the Sevii's, where likely Ponyta are smaller and slower than Japanese mainland pokemon because there are less predators such as Ursaring and Houdoom.