In the era of 2D games, vertical motion was a huge factor. There would be platforms and levels all about jumping and climbing. With 3D games and realistic environments, it has become rare to have floating platforms that were previously very easy and common. It seems like game designers have had a lot of difficulty implementing vertical exploration into games.
One game that does manage to do a good job of this is Dark Souls. Players are constantly climbing through tall structures and it gives the game an amazing feeling of exploration, sweeping panoramic views, and a feeling of accomplishment that doesn't really come from walking along the ground. What's the point of 3D games if we are ignoring a whole dimension and the unique qualities it can provide?