how about thinking outside the box on this one
instead of enclosing the animals, have them totally free, like in a wildlife reserve, and enclose the visitors in either a metal mesh tunnel or some form of clear plastic that is able to withstand tremendous impacts (plexiglass is capable of anything in SF
)
this solution allows each animal to live within its own environment, as long as you provide them with a large enough population of prey for the hunters, and plenty of flora for the herbivors.
river canyons can be created to seperate endangered herbivors from carnivors.
if the zoo is on an island, if it is large enough, a large inland sea and a large freshwater lake can be created for the (semi)aquatic creatures that are saved, although this could be left for a sequel