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I think Giovanni, Guzma and Ghetsis are my top 3 because none of them try anything special. One wants to make money using unethical means, the other is a loudmouth and the other wants world domination. They're basic, they own it and they do it well in my opinion.
The others have a weird plan "for the better of humankind" to make them more like a tragic villain, but Pokémon evidently does not have the time, budget or writers to actually make these plots work.