Animal AI - are they going to be relatively simplistic, are they going to be complex, would they learn, are they going to be capable of cooperative behavior (flocking, pack)?
Honestly, some of the more interesting "animal" AI I saw was quite a few years ago in a development version of a mini-game for "Spore." Many different levels of cooperation, aggression, flight, etc.
Plants: are they going to only grow based on their determined biome, or based on local conditions? That is, if the environment starts shifting due to drought or other climate shift, would the plants change, would which ones grow better change and thereby change the "biome?" Or would it artificially place the biome and then stamp in the right plants for it? The former allows for creation of artificial mini-"biomes" in the form of farms or greenhouses or the like, the latter might prohibit this.