>>12219553I would say the reason why the protagonist usually doesn't have a father could be one of two reasons:
1. Game Freak wanted people who didn't have a father growing up to be able to connect to the protagonist. And/or one of the story writers didn't have a father growing up and wanted to implement that into the game.
2. There's no importance/open to interpretation
I'm going with two. Game Freak never cared about the story too much. Why develop a 5-star story for a video game that is aimed towards 12 year olds?