Overall the purpose of the Meereen arc was to transform Dany into a much darker character.
With that in mind, so many of the most-criticized aspects of this plotline make a great deal more sense. Our characters are supposed to be confused and frustrated about Meereenese politics. They are supposed to hate the city and conclude that staying there is a waste of time. They are supposed to feel this generic distrust for everyone, and to fail to grasp that their peaces were actually quite successful. Dany is supposed to conclude wrongly that her behavior through most of the book was silly and foolish. And if you came away with those impressions too, its perfectly understandable.
But when you look past the unreliable narrator and POV-character bias, Martins aim becomes clear. The whole plotline is designed to maneuver Dany into a mental place where shell decide to sideline her concerns for innocent life, and take what she wants with fire and blood. Martins triumph is in handling this character development in such a natural and organic way. He gives Dany as much agency as he can her hand is never truly forced by the Harpy or slavers. He presents her with incredibly difficult situations, places her core values into conflict, and makes her choose. Her choices first go one way then another.