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For example, if I had a Female Zorua and bred it with a Ditto, would the offspring have any (excluding the usual differences in Pokemon breeding i.e EVs/Nature differences) difference than if I had a Male Zorua and bred it with a Ditto?

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If breeding with a Ditto, whether your Pokemon is male or female, it will have all the traits of both genders when breeding normally

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For Generation VI onward, if the female Pokémon has a non-Hidden Ability, there is a 80% chance that its offspring will have the Ability in the same slot as the mother (regardless of whether it was bred with a male Pokémon or Ditto).

In Generation VI, the Poké Ball of the female Pokémon is always passed down to its offspring (even when bred with Ditto); male and gender-unknown Pokémon have no effect on their offspring's Poké Ball in this generation.

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I think these are the only 2 differences, but the article was long and I might have missed some others.

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I don't think the second one is a difference because the Pokemon that isn't Ditto will always pass down it's ball
The second one says male and genderless Pokemon can't pass down Poke balls when breeding with Ditto.
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Like McRib said it doesn't matter the gender the offspring will get normal results just as breeding with a male and a female Zorua.

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This answer is wrong according to Bulbapedia.
Not what I said