I’m only doing the Arizona facilities because I’ve only been in Wisconsin for three years, Henry Vilas hasn’t changed their collection too much (I never saw the Prairie Dogs), and I only visited Milwaukee for the first time last year.
Phoenix Zoo: The Pemba Flying Foxes in the Children’s Zone. There was nothing else at the zoo quite like them, and now their former exhibit is just another ordinary aviary (that might have a rare species that I’m completely forgetting). I also miss the Elands and (this is gonna sound shocking) the Watusi in the main Savannah. They made the whole exhibit feel more busy and alive and nothing has really come in to take their place yet. I’d also say the Capybaras, but I never actually saw them.
Wildlife World Zoo: Apparently there used to be a Giant Anteater at the end of the boardwalk near the Safari Park entrance (in the same habitat that held the Spotted Hyenas before said Safari Park opened), but now the signage is gone and there’s a couple of Sarus Cranes in there instead. The funny thing is that I never actually saw the anteater when the signage was up. So was there ever an anteater in there? Was the Wildlife World Zoo trying to gaslight visitors into thinking that there was an anteater in that habitat when there was actually nothing? (Wouldn’t be surprised if it were true, tbh)
Odysea Aquarium: What happened to the Giant Isopod in the tank near the elevator at the bottom floor? That tank used to be cool and dark and now it’s a generic seahorse tank. I also miss Mighty Mike the Alligator, but I understand that he’s basically a celebrity and has other places to be

.
And while not a “hometown” zoo, I’ve visited the Detroit Zoo enough times to notice the decay in their collection, which used to have….
Asian Elephant
Hippo
Tapir
Pudu
Emu
Binturong
African Crested Porcupine
Bush Dog
Capybara
Guanaco
Takin
Elk
Przewalski’s Wild Horse
Siamese Crocodile
African Slender Snouted Crocodile
Meerkat
Fennec Fox (which I never knew they had until last year)
Drill
Lion tailed Macaque
Javelina
Arctic Fox
African Wild Dog
Coati
Yak
American Black Bear
Syrian Brown Bear
Eastern Brown Snake
Lungfish
Saddle-billed Stork
And Seals, all of which used to be there last decade (except the elephants)
Can’t have squat in Detroit, am I right?