Yeah, all reasonable points. On the whole I agree; verisimilitude is important! Overall, maybe it's just a feeling on my part, but it comes down to: a 3D map is not that much harder to implement or use, and it's more accurate and more fun to render a 3D space in a science fiction game with a 3D mode...

I don't think I've seen a 3d map of any kind that wasn't a nigh-unnavigable mess. Conveying depth is hard enough when most of the volume you're looking at is empty, and even harder when it's just a mess of lines and dots. If the map is 2d, I can look at it, and immediately plot a route from a to b, ...