Like most people here I don't have a problem with the word collection, i'm sure itcomes from a time when animals were collected, when zoos tried to gather as many rare creatures as possible, but I think the term has now outgrown this literal definition.
As an alternative (not that I need one) I think something like 'species list' can sometimes suffice, in any case where 'collection' refers to the animals kept. So when people say something like, "The zoo is ok, it's got a good collection but some of the enclosures are quite old." You could instead say "The zoo is ok, it's got a good species list but some of the enclosures are quite old." Just a thought.