Well, "capabilities" is carrying a lot of weight there. One of the main objectives is to design it for unrestricted modding to accommodate all of the wishlisted features, but "out of the box" the default game mode will be 1:1 in mechanics with some QoL improvements. The inspiration is mostly for designing systems in a way that can be easily reconfigured or extended to behave in other ways. We hope that by the time we reach feature parity, people will have already built some mods to do things that were impossible with Civ3.

As mentioned above this was started by Civ3 modders, and we all have our passionate reasons for preferring it over other entries, but you're not wrong that doing this with a 3D engine would be a whole `nother ballgame. There are actually Civ4 and Civ5 remakes underway which have both opted for 2D implementations.