I don't see the need for 3D at all. Civ is "naturally" a 2D game; the shift to 3D added nothing and IMO removed a lot. I racked up hundreds of hours in Civ 2; I'm not sure I bothered to finish more than one game in Civ 3, or even one in any of its successors.
The key graphical challenge a Civ-type game faces is conveying a lot of information quickly and clearly. 2D bitmaps are ideal for that, because sprites, tiles etc can be optimised for legibility and distinctiveness, and the fact that things are always seen from the same angle makes them consistent. All of those benefits are lost in 3D.
Civilization III was 2D as well. I agree with you though, there was something lost in the transition to 3D. Performance reasons alone is compelling argument to stick with 2D (turn wait times in Civ 5 were ridiculous). Not to mention that it's easier to create 2D art, so any mods that people created were of higher quality. There were some pretty good terrain packs for Civ 3 (for instance, http://www.civfanatics.net/downloads/civ3/modpack/Womoks_Gre...)
The key graphical challenge a Civ-type game faces is conveying a lot of information quickly and clearly. 2D bitmaps are ideal for that, because sprites, tiles etc can be optimised for legibility and distinctiveness, and the fact that things are always seen from the same angle makes them consistent. All of those benefits are lost in 3D.