The Wii U's pro controller had a glossy finish, which would lead to fingerprints and smears. The right analogue stick was directly above the face buttons, which no controller had ever done before; this made it especially hard for people who had played with literally any other controller (Playstation, Xbox, Wii Classic, GCN because all these controllers had the right stick below the face buttons).
The switch pro controller has none of these problems, but probably has a few other ones.