The protagonists of the Pokemon games are not simply mute people, they're literally silent. Mute characters still have personalities and emote to communicate, while silent protagonists are meant to have their traits and personality projected onto them by the player. Character development, by definition, for these types of protagonists has to be minimal. I think you're confusing the very few concrete traits that that the Pokemon playable characters have, along with their interactions with the plot, as character development where no such development exists.
Take, for example, Lucas (the male hero from D/P/Pt). He shares a few concrete personality traits with all the other playable Pokemon protagonists. Namely, he likes Pokemon, appears to care for the well being of Pokemon (both his own and others), and is talented as a Trainer. That's really it. Everything else is projected onto him by the player. The plot happens around Lucas, but it is driven by the other characters. Lucas, as a character, arguably makes no actions on his own, but simply flows with the actions taken by other characters. Replace Lucas with any of the other Pokemon protagonists and it would be the same story, with the same development, with no change to the hero's personality at all. They're all the same blank slates, and thus, all interchangeable.
Therefore, if a hacker is making a game with the traditional silent protagonist, their only goal is to replicate the blank slate that Game Freak normally throws at us. The rest of the protagonist's "character development" needs to go into the plot. This is because it is the plot that will allow the player to step into the hero's shoes, and it has to be constructed carefully enough as to not break the player's suspension of disbelief, nor give the protagonist (i.e. the character, not the player) too much agency or autonomy.
Basically, the silent Pokemon protagonist should be the traditional blank slate, and the plot should be crafted in such a way that the player doesn't feel like their character is making choices on his or her own. The protagonist can hold up some parts of the plot, and affect some outcomes, but much of it should be driven by the other characters. Whether it be the evil team goading the player into some action, or the professor bequeathing upon the player a task, the plot is largely happening regardless of the player, not because of him or her.
