Being 3d doesn't automatically mean it's going to be like a FPS. It picks up that rep becaus 3d is largely being driven by that type of game. The arguement about the looks would have been applicable a few years ago. For instance, Baldur's Gate's background artistry was breathtaking, while Neverwinter Night's 3d backgrounds were horrible, and totally destroyed the atmosphere of the game, IMO.
Having said that, I bought Half-Life 2, even though I become bored with FPS after about 20 minutes. HL2's background are nothing short of stunning. Combined with the excellent sound, I was totally immersed. So, if you combine the current quality of the technology, with some good attention to quality skins for the objects, the graphics for a 3d civ would be VASTLY superior to the repetitive conventional 2d tiles. The system requirements will be lower than the typical FPS, since the objects will be rendered to a 2d look, and there won't be 3 dozen objects moving constantly, in addition to yourself moving through the environment. The consternation about 3d is just stubborn hysteria.
I hope MM and the game engine will be improved enough you can play on even bigger maps than allowed in civ3. I loved playing on El Mency's 362X362 map. Of course, 30+ minute turn waits become somewhat annoying!