One of the main things I think is missing is 3d terrain from SMAC where different tiles had different elevation. Given that SMAC was released in 2000, I am really surprised that no Civ game since then has had 3d terrain and instead stuck to the needlessly shallow hill and mountain mechanic. In SMAC in particular this was really well implemented, as the amount of energy you collected depended on elevation, and artillery did more damage from higher up. And it looked good too. Overall, I am kind of disappointed the devs stuck with Civ 5 engine as it is far far from great one.