One of the ideas floating around is that a huge war occurred a few years before the beginning of the Pokemon timeline, so a lot of the player character's fathers were shipped off to war and were killed.
Another idea I occasionally throw out there more as a joke than anything else is that the player character doesn't have a mortal father; that they are the result of some immaculate conception between a deity and the player character's mom.
I'm sure that there's other ideas as well, and people will post them.
I have to wonder though why Ruby/Sapphire/Emerald are so far the only games where you do actually have a father (though he is almost never at home, dude just sits in the Gym all day, e'ry day).