Not really much to go off of here. I feel like I recall some kind of upper class manor/hotel/castle at the start of the movie and some kind of change occurring. Maybe some kind of social revolution or people mutating. I recall an airship with some kind of scientists on board. I think the protagonist was a woman possibly looking for her son.

I say it's like Fantastic Planet but it might not be fully animated. It could be something a long the lines of human actors with heavy amounts of CG or just very out there sets.

Solved: It was The Congress (2013). A bit harder to find because not all of the movie is animated. The change I mentioned was about 1/3 into the movie after the transition to animation.