Freeciv has been around much longer without being targeted by any legal threats that I'm aware of. There have also been commercial competitors like Activision's Civilization: Call to Power and its sequel that only had to drop "Civilization" from its naming for lack of a trademark license.

I'm not sure any of those aimed to be as direct a clone of a specific mainline Civ's rules and mechanics, but rules and mechanics are the aspects of the game that are most clearly free to copy.