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It would probably be better without humans, since that way the Pokémon could assume the working roles the humans would otherwise have.
That or just have the anime as is, but let the Pokémon speak amongst themselves through subtitles. The Pokémon should be treated as recurring characters in their own right, not muted creatures that do nothing but squawk their own names and follow orders.
Seriously, that early episode with the giant Pokémon where Ash's Pokémon discuss him and their loyalties is still one of the greatest moments over the whole series. We need more of that.