1. Natural Water: Several animals won't recogngize or drink it.
The number one issue with ZT2 is the inability some animals have of recognizing natural water sources to drink even if they are knee deep in it. Take the Japanese Macaque, for example, who will delightedly wade in their hot springs and walk through shallow water but will stand and bark in complaint that they are very thirsty while sitting in a shallow pond!? All animals around them will be happily drinking (Markhor, Ibex) while the Macaque dehydrates. Fennec Foxes are a hit or miss, they may drink from it once and then "forget" how to later.
Most animals also seem to have a very narrow radius for searching for food and water. It seems as if any source is more than a certain number of tiles away they begin to starve or dehydrate. It doesn't seem quite right to create an African refuge that is supposed to have one major body of water with a thousand mini ponds and water dishes because the animals won't migrate to the source.
2. Natural forage that can re-grow.
It is exceedingly difficult to create a natural exhibit void of water dishes and impossible-to-blend-in subtrate piles. Logs are wonderful alternatives, but not the best in all situations. While it is nice, for example, if a wild horse and bison have hay and gourmet grass to much on like a treat or extra healthy food source, it seems rather bizarre that a grassland animal can't subsist on grazing on grass or plants. Once an animal eats a tuft of delicous dandelion, it shouldn't dissapear forever, it should have a period of regrowth -- it is a plant after all. At the very least, as an alternative to logs and subtrate piles, a tuft of grass that looks like grass and is self sustainting rather than an obvious mound of cut grass.
3. Fighting vs. Killing
Not all fights for mates or territory should end in a carcass. A resonable percentage should be able to run away to safety or show submissive behavior and skulk off defeated. This might help alleviate the wolf problem where you have a gargantuan natural exhibit that can easily hold two packs with some possibility of allowing the population bloodlines to sustain itself, and the wolves kill each other in fights instead.
4. Zookeepers Need Overhauling
The problem with zookeepers is that they can not be regulated to one specific job like "clean poo only", "check on animal health only" or "refill food only". Instead, in a large, as-close-to-natural-as-possible, zoo they plunk down water bowls everywhere so the exhibit looks as if it has gotten a bad case of chicken pox. Easy to keep track of them in a small zoo, but they can run rampant in a large one. The trainers can be told what animal to teach and what to teach them, so why not zookeepers?
5. Beavers build dams and...
The beaver is one of the most interesting animals because it can actually do something creative and useful in taking care of itself. The African Wild dogs have an endearing behavior of sleeping in piles and an intriguing begging/regurgitating meat interaction. Other animals could be improved with unique behavors. Meerkats could be improved by being able to dig a burrow or if their scratching had a certain percentage of fullfilling the food need. Grazing animals that paw the ground for water, could be successful from time to time if they dug in muddy patches of dirt.
6. Perpetual Poo? Why not have it break down in certain situations.
It is rather suprising that the only way poo dissapears is by raking and it never breaks down. This is not a huge problem in a zoo with a compost building, but is rather bizzare and cumbersome in a large nature preserve. Some animals will go near water at the same place and other poo everywhere which is realistic and reasonable, however, the poo gets out of hand very quickly and soon becomes impossible to deal with. Animals on an open savannah should not have to complain of poo backups. Where are the dung beetles and mushrooms when you need them?
7. The Water Brush Size.
Why does the water brush only decrease to 50% of its size while the regular biome brush can be made quite small? It makes putting in narrow rivers and tributaries more difficult than it needs to be and makes fine detailing a painful task.