I was trying to make a Romhack too, but since i have no time for that anymore, i lost it.
The Legendaries concept was:
>arceus/mew/etc are "gods creators/protectors of pokemon"
>new fakemon try are based on "gods creators/protectors of humanity"
Trio is Based on Zeus, Rá and Odin.
(Eletric/dragon, Ground/dragon, Ice/dragon)
After creating the universe, Arceus divided itself into two beings. Feral form(Gen4 arceus) and Bipedal form(fakemon). Feral created pkm, bipedal created humans.
Major legendaries:
>Promezeus (Prometeu+Zeus)
>Razires (Osires+Rá)
>Ragnadin (Odin+Ragnarok)
Minor/Roaming legendaries
>Quetzequal (americans protector)
>Oxumaré (africans protector)
>Asurindra (asians protectors)