Jimkirk, this is kinda off topic, but here are aa few ways that I can think of off the top of my head.
First, it allows an near infinite number of zoom levels.
Second, it allows for nearly any screen resolution.
Third, it simplifies unit creation. Really. Currently, the artists build 3d models and animations for the units. These are then rendered out frame by frame to the 2D animations and then cleaned up. This would cut out that step. You can also have more detailed animations, as techniques like skeletal animation are available to you.
Fourth, on modern systems, 3D graphics have less CPU overhead than 2D as the video card is doing a fair amount of the work. This may free up the CPU for important things like AI.
Fifth, you can make more natural looking terrain, with rolling hills and plains of various heights, rather than picking between a few hill tiles or plains tiles.