1. Is there any way getting Butterfree back or I should just avoid giving it away in the mating event thing?
2. In SS Anne, there's a guy asking you to trade your Butterfree for a Raticate. Since Ash refused iirc, why not make the player refuse automatically here too?
3. You should set Bulbasaur and Squirtle's level requirement for Ivysaur/Wartortle to something like lv55-60, so they WILL evolve by themselves after the league but (most likely) not before it. Also, you should set Charmander to Charemeleon's requirement to level 3x or so, then Charizard's requirement to something like 3-4 levels after that. It just feels wrong to repetitively press B after every level for 3 Pokemons, or cheat for everstones, to get the appropriate result in comparison to the anime.
Oh, I have an even better idea for Squirtle and Bulbasaur: make a "What-if" story for the Orange Islands, once the player finishes the Orange league (the one where Charizard beat Dragonite, if you're going to do that). So once a player finishes the game, he'll find 2 special gems or something, that either evolve them or just allow Bulba/Squirtle to evolve.