I believe 3D graphics is here to stay even for games that do not need 3D for gameplay reasons (like Civ). The reason is, it is becoming much easier to create nice and arbitrary looking landscape by using in-built effects like dynamic lighting, shading etc. Animations are much easier to realize in 3D.
2D graphics need either be painted, which is laborous, expensive and inflexible or pre-rendered, which seems kinda unnecessarily inflexible because even low-budget laptops have the graphic processing power to do this real-time.
However, these advantages of 3D invite to pay less attention to the artwork (Models and Textures) which might result in 3D looking considerably worse than 2D - but that is not a problem of the technology but rather of priority in game design.
they cant make the game world, cities and units high poly at all, thats the problem with 3d and games like this. Sure for awhile its fine, but what happens when you have 200 units and 100 cities if the models are more than 200-500 poly? I know your system slows to a crawl more so than it already does. 2d can still have nice looking units for a game like this. 3d in this instance requires less work from everyone concerned