I had some other thoughts before but scrapped them. I left some in the spoiler below.
If we can just convert all the old pokemon to the new version, most of the work is already done.
Just segregate some civs of pokemon of the same type. You could probably put the gastly line into poison, dratini line into normal, reduce the amount of necessary civilizations. You could also go by team instead, maybe a team rocket civ with mons used historically by team rocket members.
To make a creature for a pokemon civ, you have to define a new pokemon creature with castes of each pokemon that can live in the civ. So the fire civ would have vulpix, magmar, and growlithe castes. We could use the type guidelines of the pokemon TCG, with rock, ground, and fighting types in one group, ice and water types in one group, dragon and normal types in one group, etc.
For humans, try to find a Japanese language raw file someone else already made for DF, if you want the flavor. It should be as simple as removing their basic attacks to neuter them. Probably remove the other civilizations, since we're using pokemon civs instead. We probably do want multiple hostile human civs so that we can have pokemon battles.
The game would be like the world of Sir Aaron and the
Red Army. Humans and pokemon fighting each other to death, in armor. Pokemon being sentient and capable of organizing themselves, some of them might not wait for human orders but form their own warlike civilizations along mystery dungeon lines.
Some pokemon will have COMMON DOMESTIC to make all human civs bring them, and other wild pokemon can get tamed as necessary.
The first part is to decide what the scope of the game is. Probably just the 151 lines + some favorites like the Latis, Celebi, other gen starters/legends, with more to be added later.
You'd want to make each pokemon essentially the same at base level, modular so you can customize their bodies, attacks, and castes more easily. You probably want a representative attack of each type you can copy paste between pokemon if you're doing this from scratch. I don't know what there is in the other mod.