3D maps are obviously another dimension of complexity and can be a bit disorienting when viewing as a 2D projection.
SC1 and SC3 both used two-dimensional projections of a spherical three-dimensional star cluster, which weren't impossible to figure out but were a little confusing as they weren't true 3D so it was often difficult to tell how far your position was relative to other stars, which I think is something of a barrier to gameplay immersion.
SC2's flat map may seem "dated" but it's easy to comprehend and there are many modern games that take place in space and are fully realized in 3D, but use 2D map layouts. Just look at GalCiv where everything is built in 3D, but most of the action is effectively restricted to two planes to simplify gameplay.
I think a 3D starmap has the potential to be cool but not necessarily in the spirit of Star Control (more like a space combat sim) and would potentially just over-complicate the game. Not saying it couldn't work, but such an approach would also require a lot more design effort and may not fit into either the game's budget or design ethos.
Any thoughts, Vaelzad?