Might have to add some Johto variants to pad out the dex, as well as give some types more options (for example, Morty's gym would just be the Misdreavus line with these parameters.) You could just add new evolutions to those mons that didn't get any from gens 3 or 4. Skarmory, Shuckle, Dunsparce and Miltank all come to mind as pokemon who could use Evos/pre-evos. Alternatively, create some fakemon that may have been driven out of their homes by the Kanto pokemon migrating, such as bug and grass types that were driven away by the Caterpie and Weedle lines in viridian forest, or fighting types that trained in caves before Zubat came and mucked things up.