Almost all major zoos are public - by which I mean they are city/state properties like parks - and depend on public funding for the majority of their money. Tickets and donations are usually a tiny percentage of the zoo's funds. There could be a way to mimic that in the public system - a yearly amount of money received based on your inspection report and/or guest numbers or similar. As it stands, so much energy has to be devoted to human management when the game should really be just about the animals 
I've also noticed (as a newbie to the franchise mode) that a lot of players breed randomly and dump their poor choices on the market. Reputable zoos are all members of various zoo associations (AZA for America, similar for other continents). I could see a function where if a player has good zoo maintenance and appropriate breeding practices (less than 10% inbreeding/genetic averages above x/whatever) you 'join' one of those organizations and get periodic access to system generated animals that are decent quality. Maybe even an 'elite' level for people who keep and breed rare animals (thought that would mean adding a 'breeding difficulty' to various animals).
I've also noticed (as a newbie to the franchise mode) that a lot of players breed randomly and dump their poor choices on the market. Reputable zoos are all members of various zoo associations (AZA for America, similar for other continents). I could see a function where if a player has good zoo maintenance and appropriate breeding practices (less than 10% inbreeding/genetic averages above x/whatever) you 'join' one of those organizations and get periodic access to system generated animals that are decent quality. Maybe even an 'elite' level for people who keep and breed rare animals (thought that would mean adding a 'breeding difficulty' to various animals).