I don't think commonness or realistic presence of animals in zoos should be a criteria or limitation at all. As mentioned, the game (in theory) allows you to build zoos in any area of the world so an animal that isn't found in captivity in one part of the world may be more present in another.
Second, zoos are - more and more - becoming the last refuge of desperately endangered animals and I think we're going to see more and more of that as habitat degradation gets worse. A classic success story are the California Condors - on the surface not a good zoo option; needs huge territory, we hadn't bred them very successfully, etc but it was determined to be the only way to save the species, and we did. Now they are present in several US zoos, and that is pretty much the only way the species survived. Maybe it's hard to keep so-and-so animal in a zoo but, frankly, in increasing numbers of cases, that's the only way they have even a chance to survive (the little Mexican porpoises spring to mind - as they're attempting to capture the last few survivors for a captive program - but I think we're too late for them).
Finally, of course, ... it's a game and this is an area where I don't think we need to hew to realism.