Building on what LH said, if you really want something that's 3-dimensional to the likes of 4/5th gen, you merely have to artistically think 3-dimensionally. This will probably always be my favorite example:

(Spherical Ice's Pokemon Gaia)
The slab's 2D, but the orientation of it and its surroundings give it something of a 3D appearance. And I'm not saying it's easy to do or even that things other than this, like trees and grass won't prove more challenging, but the DS Pokemon games are very 3D-lite and unexceptional in that area, and I'd think it not impossible to rival or surpass them in making something that simply looks 3D.