All of'em I believe. From the top of my head:
Dragonite Family, Garchomp Family, Salamence Family, Druddigon(Late game from Dray.), Swablu & Altaria, Flygon family(Trapinch in the dessert after the 4th city.), Rayquasa(from the missing relative), Dialga & Palkia(Late game), Haxorus family(Axew in 2nd region.), Hydregion(Deino in 2nd region.) And I'm sure there's others I'm just not remembering.
I already have the story all formatted from the original version of the hack I did last yr that was completed, but it's way too glitchy to play. So I'm transfering information from that rom over to this updated one.