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Masuda’s greatest flaw as a writer/game designer is that he sees the antagonists as the conduit for the plot/themes of the game rather than seeing the entire game itself as the conduit for the plot/themes. This is why he can write compelling antagonists like Cyrus and N while also writing one-dimensional rivals like Cheren and Bianca who are supposed to be your childhood friends, except no flashback sequences or memories are ever brought up to actually sell the player on their character’s relationship to them.
In the same vein, Team Plasma are supposed to be all-encompassing and culture-altering but you never actually see the cultural landscape of Unova change or the attitudes of the characters change. In Colosseum you have entire towns under the control of Cipher, in Mother 3 you see your hometown change over time, in Pokemon Black and White you’re required to visit most of the cities a single time and then never again, and Team Plasma’s presence is only wholly felt when Ghetsis or N gives a speech or encounters us in a cutscene.