The different varieties of the same type (lemurs, gibbons, etc) should just be distinguished in their detailed description like humanoid hair/eye colors or as castes; not treated as separate species.
That's a cool idea. Alternatively, maybe they could have what they are in a general sense in brackets. For example: Kea (Parrot). That way it's not hidden away in the detailed description but it's still easy to find out what it is.
Personally, I really like the animal variety in Dwarf Fortress. It's interesting and flavorsome, and occasionally educational. Not so much a fan of the "giant" variants since they often don't make any sense in biological terms, and that seems out of place in Dwarf Fortress.
Re: the wandering animal men - I think it'd be nice if the animal men were all historical figures in some sense - that there was a specific number of them around and they didn't just bumble around the map like a generic animal. When I see a group of them roaming the map like an animal it's a bit weird, but when they have a camp in the caverns or something that's really awesome. In a recent fort there was a little tribe of... cave swallow (wo)men? They ended up getting into a fight with a forgotten beast and all became weapon masters by the time they killed it. That was spectacular and very worth having in the game.
First off, if animals that are separate species are made into castes, won't that mess up how they reproduce?
Secondly, I agree that animal men need some sort of narrative behind them. What events bring them into being? What is their goal in life? It would make a lot of sense if animal men were created individually or in groups as a result of
specific divinely- or demonically- influenced worldgen events, similar to necromancers. The animal men could be transformed sentients living under a sort of curse; one example that springs to mind is when the Greek goddess Leto transformed the Lycians into frogs as a result of their having insulted her. There are thousands more stories like this in all cultures' mythologies.
Another option would be for animal men to serve as a sort of immune system for nature- if your hunters kill too many animals, or kill them in a specific place or way that is offensive, it causes the animal men to emerge and take revenge either on your entity or on the specific offending hunter. In this scenario, the animal man is sort of like a belligerent Lorax rather than a species per se; they would be called into being via spontaneous generation or through a nonsentient animal being transformed somehow, similar to night creatures. The essential weirdness of animal men is done a disservice by having them just wander through maps behaving as if they were any other animal except un-butcherable.
Finally, I think that it would make sense for each animal to have a tag identifying its ecological niche, and to restrict the number of species that occupy the same niche in any given biome. This would permit diversity but you would not get cheetahs, cougars, leopards, lions, jaguars and tigers plus giant versions of same all together in any given tropical shrubland biome because the biome can only support one or two kinds of animals that fill the "solitary terrestrial carnivore" niche or whatever.