Hmm, animals that are present in many zoos but still not well represented overall?
Equids. We have just the one zebra species.
Procyonids. No coati, raccoons, or ringtails.
New world monkeys, baboons, and gibbons are species seen in many zoos that are (except for the Capuchin) absent.
Birds. Even without an aviary pack for flying birds, there are a number of wading birds, ground birds, and waterfowl that are commonly kept in open or covered habitats (including walk through ones) in real zoos. Lots of zoos have those. We have relatively few bird species overall compared to mammals, or even reptiles. Kiwi are rare in zoos overall (and pretty shy), though a few have them. And it would be nice to have something from New Zealand.
Tayasuidae (peccaries) aren't true pigs (we have two suids so far in game). They'd be great in a desert pack as a new world representative.
Armadillos and sloths are present in many zoos.
No porcupines.
More marsupials! Wombat, tree kangaroo, bandicoot, cuscus, possums! These species aren't found in all, or even most, zoos, but for folks who do want to make a more regional Oceania type zoo, they make sense.
Except for the two otter species, we have no mustelids. No skunks or civets either.
Giant snakes like pythons, green anacondas etc. Maybe a similar issue to flying birds, though. The current game mechanics, with 4x4 exhibits or open habitats with no in between, make it hard to put them in the type of enclosure one usually finds them in.