I think this is the maddest a Pokemon game has made me, as far as narrative goes. Up until this point the rules were you beat a trainer, they give up and give you what you want. Sure it was strange that grown men and women, organized criminals, were bending to the whims of some random kid but I grew to accept it since it happened in every game. I figured they were afraid of being attacked by the player's Pokemon directly. Who knows what the MC is thinking, kid could be a total sociopath for all we know.

But then these two Plasma thugs show up. Even after being soundly beaten in battle, they keep on beating Munna to make it fart magic mist. You did what you're supposed to, you followed the rules as they had been established up until this point, but it doesn't matter. And there's nothing you can do about it.
What would have happened if Musharna hadn't shown up? Would the thugs have beaten Munna to death? Would the player have intervened? Would your Pokemon even listen to you if you told them to attack a human being directly?

I wish Pokemon had more subversive moments like this, things that make me stop and wonder just what it is I'm trying to do in this game. The rest of the story with the whole "liberate your Pokemon" thing kind of goes for that but to me it fell rather flat, largely because the idea of Pokemon being your friends rather than tools is completely at odds with the gameplay mechanics. But this one moment stood out to me, and replaying the game now it still gives me pause.