I'm not sure why Smith couldn't just do his copy thing over each of the 666 beasts one by one.
Since I believe the reason you can't defeat the guy without continent destroying power is because you have to beat all of the beasts at once or they regenerate. Copying himself over the beasts seems like a strange alternate way to defeat them that I'm not sure they'd be able to "regenerate" from.
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No problem!
This is a cute and pop genocide of love!