True, Jigglypuff wasn't really a Kirby clone aside from being a ball that could jump 5 times but I think they chose her because she would be much easier to make as a ball character than say, Meowth or Mewtwo who would be more complex with their tails, limbs and projectiles.
I'm not really knowledgeable about it, but I read somewhere that during the making of ssb64, Pokemania was at its highest in Japan with Plush dolls being sold everywhere and that puff was one of the most popular. I bet if smash 64 wasn't originally meant for Japan only, then they would've reconsidered having Meowth instead of Puff since he's far more popular and recognisable in America than her.
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