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After spending some weeks overanalyzing the plot of Gen 5, I have come to the conclusion that Team Plasma makes the most sense as a stand-in for Abrahamic religion, and that the Black and White duology is not just about the ethics of Pokémon, but rather a big middle finger towards the desert religions that have historically dominated the west, much like how DPPt was basically denouncing monastic Buddhism throughout Cyrus and to a lesser extent the rest of Team Galactic.
You can notice this from the visual and literary aesthetics that Team Plasma uses alone, what with the original Team Plasma resembling Crusaders, and N being portrayed as some sort of Messiah-figure. In the second game, the old Team Plasma splits in two, with the side that sided with N secularizing as they start interacting more with the world outside them while Neo Plasma goes down the road of fundamentalism, living in a mobile ship (basically refusing to interact positively with the outside world) and doubling down on Ghetsis's (who might as well be the cult leader) rhetoric of taking over the world (jihad).
In a way, Black and White were basically Game Freak's way at getting back at the Christians who denounced the series all the way back during the Pokemania days, and I'm all up for it.
