>>30787195A few comments.
Metagross line should be a natural machine. It follows those traits far better than it does things like Chimecho, to the point that just like Magnemite and Klink, its evolutions are literally just conglomerations of individuals.
Paras may warrant a special link between fungi and where it is.
Gyarados and magikarp present a problem, since Gyarados doesn't really fit with fish, and Magikarp doesn't fit with snakes or dragons.
A possible answer could be creating a branch off of Fish that just has sea serpents in them. It may or may not branch off into a few other dragon families as well.
Charizard and Garchomp need to break off separately from Axew and such, probably closer to the bagon line.
>>30788030This is very good. I like this.
On to pure autism with the legendaries, much of which is unsubstantiated headcannon.
Deoxys and Palkia have nothing to do with eachother.
I believe it wouldn't be outlandish to suggest Palkia (matter) produced Groudon and Kyogre. Groudon would likely then be subsidiary producer of Regigigas, and maybe Heatran (Heatran may also fit into Dialga's pantheon, or into Zygarde's subgroup), while Kyogre maybe produced Manaphy.
Dialga (Time/Energy/Change) would likely be the producer of Articuno, Moltres, and Zapdos (Remember the birds correspond to the changing of seasons)
Giratina (Balance/antimatter) I could see as responsible for the likes of Lugia and Rayquaza
Zygarde is basically the will of the planet. Enough energy and matter came together making the planet that it developed a consciousness unto itself, and needed a way to act on the world. Zygarde is thus technically a creation of Arceus/Creation Trio, but an independent one.
Heatran may also fit here as a sentiant heart of a volcano.
Hoopa might be outside of Arceus' creation entirely. Hoopa might have literally poofed itself into existence.
Deoxys is unkown. It's from elsewhere in the universe, put it with the aliens.