If you're still having trouble with categories then I would suggest either deviding them by chemical make up (carbon based lifeform etc) or primary method of obtaining energy (photosynthesis, consumption of other entities, other chemical processes) as I can see both of these categories having a large affect on behaviour.
I'd like to find out how you will categorize your animals. What I imagine is probably a little unwieldy to actually code.
This is, essentially, what I settled on. After a long talk with my girlfriend the Bio major, I decided the only sensible way to start out categorizing creatures would be to separate them by diet. What I've got for basic groups are Carnivore, Herbivore, Omnivore, and Other. Other will contain the weird odds and ends (creatures that gather their energy from crystals deep in the earth, creatures fueled by magical power of one type or another, creatures that are direct energy producers, and so on).
After separating them by diet, they're further separated by sphere: Terrestrial, Aquatic, Aerial, Amphibian, and Subterranean. Each of these categories will have a slightly different procedural generation. The chance of a creature being one type or another is all simple weighted random choice, so a world might end up with barely any terrestrial predators, or an overabundance of them. Spheres will also experience some degree of crossover (terrestrial creatures should still be able to develop wings, a la dragons). After these basic categorizations, further specializations, traits, and terrain specializations will take place/be added, along with the actual physical morphology. Morphology should, to the point of being able to suspend disbelief, make sense for the creature's biome and habits. Creatures should still be able to inspire a 'what the hell is
that?' reaction from players, however.
I've retweaked the terrain generation once again, although I've also made some decent progress into beginning the Creature Gen section. I wanted continents to look less like they were created specifically to fit in a box-shaped region. It isn't perfect, but it's looking somewhat better than before. Also, I wasn't liking the 'stretching' effect around the edges of oceans that was being caused by ensuring that map edges are water tiles, so I adjusted things to (hopefully) make them look more like natural continental shelves.
Worldgen has been significantly sped up by algorithm changes. Anybody with a 2ghz+ processor should do just fine with the generation process, and the heavy lifting sections are pretty much done. Older cores will probably still be fine, but there may be long-ish waits involved.
I'll post some teaser images if I have time before I run off to work.