On the ark issue, as a programmer I'd probably approach it a bit differently.
It's impossible to figure out what mods people will install. You can't work out all interactions if you can't know what the interactions might be, and in a game so focused on modding, it'd be silly to build a whole solution around the ark that doesn't work for a mythical ark, or an extinct ark, or the combination of two of them. Personally, I'd add tags to the species that describe their overall characteristics that have an ecological impact. We have size and damage, litter size, but no other reproductive rate (gestation, that kind of thing). I'd add herb-, carn-, omnivore, can_scavenge, and some things like that. Ignore for now the broader ecological predator/prey population modeling for something simpler.
Prior to world gen, I'd dump all these species the user has selected out onto the world and do a quick ecology model mostly independent of the civs placed down. It doesn't need to be global, maybe just one per biome combination, and only for the purpose of getting entity balance down. Something like a virtual arena.
In each setting, iterate over each carnivore and pit it against each other creature in the biome (including a dwarf peasant). If it's a pack animal, pit them as a pack. Work out a simple success ratio over a number of passes, normalize it, and use that to determine hostility toward those other creatures during world gen and the game. Let's call that the hunting table. Do the same for omnivores but add in the variable for them to go vegetation only during the game. On a mountain, they'll be carnivores, on a savanna they'll probably be herbivores. During the game have each wild animal seek food each season using the probability model and what they can actually find, during world gen, use the probability model to work out appropriate populations for each species rather than trying to manage it at the individual level.
The advantage to this is that once the tags are in there, the animal interactions can be established largely outside of gameplay just by having a reasonable model, which means that the community could help build and test the model for Toady. He'd have to do the in-game animal behavior, but the rest could be done as the OpenGL work was done. Plus, if you have an external simulator such as this, modders have a means to test the interactions. If big cats aren't willing to hunt a large hoofed animal, perhaps the hoofed animal is too strong, or the cat too weak. The simulator would help create better animal mods. I think this is what Vicomt is nudging toward.