I love games with 3D environments. Some of this is from having read Ender's Game as a child, and the sheer awesomeness of the main character's solution to how one orients oneself when there is no up and down. How does a person move and coordinate with others in a place where there aren't any of the directions that life has accustomed us to?
The answer, of course, is to create your own frame of reference. One that maps the old sense of direction onto a new environment in a way that opens up new possibilities.
I also love such games because they push us players to transcend the 2D environment that shaped us. Sure they're uncomfortable at first, but any sort of transcendence, even a little one barely worthy of the name, requires doing strange and sometimes disorienting things. It's a part of pushing past the narrow points of view we all start out with in life. Views like the limited framework terrestrial evolution has gifted us with, if we want to move onward and outward into the universe at large.