Well, in my opinion. It's not so much what animals they have, more about how they have them. Welfare standards are key in making a zoo good or not. There are a few out there whose standards aren't up to scratch and are well known for it.
I think, also having well designed exhibits is important. To be able to balance the visitor needs with the animal needs is important so to have an enclosure that allows good viewing, but also lots of places for the animal to have some privacy, means that the exhibit has been well thought out and designed.
Also, good facilities are important. If the café is rubbish, and the toilets are awful, then it sort of ruins a zoo which is good in other aspects.