I'd actually replace the Magikarp event with a Feebas instead. Just don't give the player a prism scale until later in the game. That way you can't get access to an OP, bulky, hydro pumping, recovering, monstrosity until it's actually appropriate. This would also mean that for a good portion of the game you have actually wasted the precious money you start off with buying a pokemon you can't use at the beginning of the game. It'd also solve the Gyarados is too strong problem. The more I think about this, the more sensible it seems.
Pokemon Reborn: Budew Edition needs to be a thing that is developed in secret and sent to Ame as a tribute once the final episode is released. Imagine her walk into the starter pokemon room and every pokemon is Budew.