I’ll tell anyone who has ears that Pokémon Gold/Silver/Crystal are my favourite Pokémon games (Silver is my #1) but I never really considered the games to have the best Pokédex. Cian Maher believes Gen 2 did and wrote about it for The Gamer where he listed his “best” Pokémon from the gen and compared it with other gens. Gen 2 won out.
I’m often accused of being a dirty genwunner, which makes sense given that six of my ten favourite Pokemon – Squirtle, Blastoise, Vaporeon, Gyarados, Haunter, and Arcanine – all come from Red & Blue (the other four are Suicune, Primarina, Absol, and Umbreon). If anything, this just testifies to how truthful I’m being when I say that Kanto only ever had the best Pokemon when it was the only generation available to play. Three years later, when Pokemon Gold & Silver first graced the world with their inimitable presence, everything changed, to the extent that we’ve still yet to see a better regional Pokedex over 20 years on.
While many would disagree (especially because Gen 5 got the lowest score from this measurement and everybody loves Gen 5 for some reason), this is clearly an opinionated thing and better suited for a “faves” list rather than a “best”. But Pokémon wouldn’t be Pokémon without arguments and Cian clearly stated at the end that he didn’t care so that’s that.
I may do this myself and see which generation wins out. My bet is on Red/Blue/Yellow (I’m a casual genwunner).