Love him, simple as that. I've always liked Giovanni. His big plan wasn't to summon a legendary Pokemon and try to change the world with it. He took over Silph company, the company that literally makes Pokeballs and Potions and basically fuels the economy in the Pokemon world. Rule the world with money, that's why I've always liked Rocket.
Having him as a gym leader was also a pretty nice touch.
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He can be intimidating, but Giovanni isn't even close to being the be-all-end-all villain of the franchise:
*In the games, runs to his Gym to hide after losing twice to the same Trainer, then flees out of shame after losing to him a third time. Gets humiliated again by Ethan three years later, rubbing more salt in his already-festering mental wounds.
*Funds Mewtwo's creation in the anime, and all he actually does with such a powerful Pokémon is to have Mewtwo psychically immobilize wild Pokémon for easy capture (talk about a waste of potential).
*Spent the majority of his anime "appearances" being the object of Meowth's overexaggerated fantasies. What few times he appears in person is usually just to grumble and snap orders at his agents.