I submit that creatures be given "biome" distinctions as well as "predator" and "prey" lists to determine where they are in the food webs of each biome. We can determine this in the following manner: In area mode, an amount of the new species equal to the size of that creature is pitted against up to five other species of creature.
Each Creature must be pitted against one or more creatures whose total Sizes equal theirs (ie: 3 "Size 1" creatures vs 1 "Size 3" creature)
The creature or creature group that survives combat in a minimum of two or three arena mode contests becomes their opponent's "predator", while the one that is killed a minimum of two out of three times becomes their opponent's "prey".
For each new predator added to a species' list, they should gain +2 mutations available, while for each new prey added to a species' list, they should add +1 mutation available. In this way, successful predators will maintain their basic shape much more than prey animals will and the frequency that any specific creature enters contests determines how specialized their diets will be in the resulting food web. (Pandas and mosquitos anyone?)
Animals with the "Grazing" tag (ie: herbivores), could still contest to be considered prey or not, adding a mutation for NOT becoming a prey animal rather than actually adding their defeated opponent as "prey".
Pretty soon, a food web would emerge and this kind of thing could be done for each biome too, unless really successful species attempted to "compete" in other biomes as well (adding a biome tag to their description).
It could be really fun. Sorta like "fantasy football".