I'm currently happy with what we've got, but if I had the choice...
Zoo Tycoon 2: Instead of a Dromedary Camel, I'd have a Bactrian Camel, because (unlike the Dromedary) the Bactrian is still a wild animal and fairly endangered as well. Besides, mosts zoos with camels have those (the ones I've been to anyway). Instead of a Mountain Gorilla, I'd have a Western Lowland Gorilla (for realism).
Endangered Species: I'm not willing to remove an animal just because it moves wierdly or looks ugly, but I would be willing to replace the Javan Rhinoceros with an Indian Rhinoceros, or even a Sumatran Rhinoceros, both of which are endangered themselves, but still kept in captivity. Also, although it is South American, I wouldn't have a Baird's Tapir. I'm sure there are rarer breeds. A Malayan Tapir, like the last ES, would have been cool.
African Adventure: First of all, I'd like to state that I don't exactly see what everyone has against the Masai Giraffe. So there's two subspecies of the same animal...it's really no different from the original ZT having both Bengal and Siberian Tigers, which I don't remember any complaints there (OK, yes, they were of different biome, but the point still stands). I don't have a problem with most of the other animals either, as a lot of them are animals you do actually see in zoos. Even so, I think a Crested Porcupine would have been nice. The game really lacks rodents, and what better than the second largest in the world?
Marine Mania 2: I'm not fussed with most of the animals (I was hoping for a more realistic penguin from day 1), although there is still room for improvement. Animals I'd replace would be the False Killer Whale and maybe the Short-Finned Pilot Whale. Certainly the former because it just doesn't really have the per-zazz as the real Killer Whale isn't called that in the game. I'd replace it with a Marine Iguana. If the Pilot Whale would be replaced, I'd have an exotic bony fish, like the Ocean Sunfish or the Coelocanth. I doubt they're captive-equse animals, but they're cool.
Bonus Downloads: Of the four downloads so far, I'd probably replace the Black Leopard with an actual breed of Leopard, like the Amur Leopard. The black leopard could be an alternative skin for it.
Dino Danger Pack: Keep the T-Rex and Triceratops, but replace the Carnotaurus with a Velociraptor and the Styracosaurus with a Stegosaurus, for variety sakes.
OK, that's all.