IMO:
- Leave the 100 pokemon that were introduced for the 2nd generation in the dex and have them ALL appear before the player challenges the Elite 4.
- Dump about 75% of the Kanto pokemon and just leave stuff like Magikarp, Geodude, or things related to the 2nd dgeneration like Pikachu(Pichu), Magmar(Maby), and Bellsprout(Sprout Tower). Pidgey and Ratata need to go. Random pokemon like Meowth, Drowzee and Tauros need to go.
- Add the Hoeen and Sinnoh pre-evolutions and evolutions of the Johto pokemon. Azurill, Magmortar, Yanmega, Bonsly etc.
- Add a few Hoeen and Sinnoh pokemon, but very little. Just enough to make the gym leaders and Elite 4 members teams interesting. For example, instead of Gastly, Haunter and Gengar, Morty's team can be Misdreavus, Dusclops and Gengar.
- After the player defeats the Elite 4 they should get the NationalDex which has all 493 pokemon in it. Many of the Kanto pokemon should be obtainable when they make their trip to the Kanto region. Additional Hoeen and Sinnoh pokemon can be found via swarms, PokeRadar or other special events in Johto AND Kanto.