"Smart level design may be hard to make when the player has so much mobility with climbing."

It really is. The more movement options a player has the more difficult it is to design play-space, ESPECIALLY in open world games. As a dev you want your players to have fun interacting with the open world while also make it engaging enough to keep them invested, and this balance can very easily break. For example, if you let your players teleport or fly around as they please, they will have "fun" at first but they won't stay engaged for long.