I don't know why, but the only relatives that we have in the games is.. our Mom.. except in Gen III
Blue's grandfather is Professor Oak..
Silver's father is Giovanni (Quite sad when I read about it in the Manga)..
In the Gen II (If I recall) and Gen IV of G/S, our 'friend' or should I call Crystal, have parents, grandfather and grandmother..
In the anime, Barry's father is Frontier Brain Palmer
It seems that the playable character got quite left out in the 'family' part.
Either way, my theories are this;
1. died
2. being a trainer on a journey
3. somewhere in unknown-to-us regions
4. imprisoned (there's prisons in the Poke world? ._.)
5. left out by Gamefreak
6. divorced
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I think that the first gym leader you met is your dad and I mean met not fight so they are:
Brock, Falkner, Norman(of course), Roark, Cilan.
It is always a male gym leader you first met.
You're kinda missing it out on the Unova part. You forgot the other two Gym Leaders.. Chili and.. (forgot his name). If yur theory is true, then what could be worse than having 3 fathers? LMAO ! O.o