Was it really a plot twist in that case though? Movies with a mystery/conspiracy plots obviously have someone who's behind it all. And if you thought the mayor was the real villain when he was arrested with like 40 minutes of the film left then you're probably an idiot.
I mean, Disney has been using the whole "character who seems nice is actually villain" thing too much lately, but at least in this case it wasn't really done in a HA TRICKED YOU way like Frozen. There was obviously a villain working behind the scenes in Zootopia that the characters hadn't discovered yet, the seemingly friendly/put-upon character turned out to be it.
I don't think Zootopia was a masterpiece but it handled that aspect better than Frozen did.