I would greatly prefer to have Meowth over Puff. I can see why Puff was chosen at the time - she had a pretty large role in the anime and was pretty popular, and since Smash 64 had a budget of pocket lint, could be built off of Kirby. There really weren't too many other Pokemon at the time who could be built off of existing fighters, and of the ones I can think of, they'd be worse additions than Puff.
It's only in hindsight that Puff becomes one of the worst additions in my eyes. Gen 1 is the only gen to have more than 1 fighter from it, and boy does it have a lot. However, each gen 1 mon is easy to justify, except for Puff. Pikachu is the mascot, Mewtwo is the only legendary and serves as the "villain", and Pokemon Trainer incorporates stages of evolution and switching and serves as an excuse to add Charizard who is the series' other mascot. That leaves Puff feeling very superfluous, as her gag in the anime isn't really used (they revived it briefly in Sun and Moon but it didn't shoot her to the top of popularity or anything). In the mainline games, she's never really been more than a random Pokemon you could come across. Her popularity really faded after gen 1 and never really picked back up much. Meowth has at least remained relevant in the anime as well as the games (he's gotten the lion's share of new forms the past two gens!)