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I know in gen3, the dad is a gym leader, which makes sense. Am I missing on the details why the dad is never present at the beginning of any of the games? (Excluding Ruby, Sapphire, and Emerald)

Maybe the creator of Pokemon had daddy issues.

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This is currently unknown.

It was never confirmed that the played had a dad either, excluding in R/S/E. We haven't received information on a father even if he did exist either. This may be due to a lack of roles for the father to play; the mother already sets you up to play the game at the beginning of the game.

However, certain characters such as Bianca clearly have a father, so it can be assumed the player has a father; though his whereabouts are currently unknown.

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"The character has a father"
Nah, you're a clone.
Divorce, maybe?
could even be adoption