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I personally like Giovanni because he is so down to earth. He's not some Saturday morning cartoon villain who's trying to destroy everything or rule the world, he's just a humble crime boss who creates a lot of havoc and is also the final Gym Leader of his region, which was a really cool twist in Gen I. Being the father of Silver made him even more of an interesting character. Looking at the other villains:
Archie/Maxie:
>I want to use the power of the legendary Pokemon to increase/decrease Earth's landmass
Cyrus:
>I want to use the power of the legendary Pokemon to create a new world
Ghetsis:
>I want to use the power of the legendary Pokemon to rule the world (literally the most boring and cliche motive possible)
Lysandre:
>I want to use the power of the legendary Pokemon to power up the ultimate weapon
This same formula is a bit stale at this point. Ghetsis seemed like a really good villain early on in BW with all the Pokemon liberation stuff but then GF decided to flush it down the toilet and just make him the most generic villain possible. He's still a cool character with how he brainwashed N and generally comes across as a really evil guy but there's just so much wasted potential going on with him. What a shame.
Now, Lusamine is one of my two favorites since she breaks out of this usual motive too. The way she talks, her facial expression and her "private collection" of frozen Pokemon among other things all make her seem like a batshit insane person who has completely lost it. She's not trying to rule the world or any of that shit, she's just obsessed with Ultra Beasts to the point where she snapped and even rejected her own family. I think she's a great lunatic villain who even manages to be a bit disturbing and scary at times.
tl;dr Giovanni and Lusamine are my favorites, followed by Ghetsis, followed by everyone else.
