>>35367875I mostly agree with what you're saying there but as you point out, the name of the game is Pokémon. THEY are the true main characters so having plots revolve around them makes the most sense.
The only real problem I see with going along in this line is that it's also against the theme of the series. Pokémon aren't inherently bad for the most part as even the "evil" ones are most often just misunderstood, like Absol or tricksters like Sableye. Even ones like Sneasel/Weavile which are portrayed as ruthless really aren't. "Oh, noes! You're an animal eating other animal's eggs as food." Yeah, that's not evil.
In essence, Pokémon should be the big bads because they're the stars of the show, but they can't be. So it falls to human characters to be the bad guy.
Now that I think about it, that's probably why the Mystery Dungeon games are a little better, since Pokémon can be bad there (though they often turn out not to actually be, or get fixed along the way which kind of drags them down).