I think the Pokémon version of a zoo is indeed the Safari Zone. 'Cause here's the thing, in Generation I... in Fuchsia City, it had Pokémon in enclosures just like any ordinary zoo would have. Then of course... the actual Safari Zone game
is actually the open-range zoo, Pokémon style! Hence that is why it's called the "Safari Zone". xD
But yeah, it's something I would love to see return in Pokémon X and Pokémon Y.